Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014579.1 Kokia drynarioides strain JFW-HI SEQ_129618, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 224217
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Warning! 21 characters in sequence are not A, C, G, or T
Found at i:3163 original size:6 final size:6
Alignment explanation
Indices: 3138--3176 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
3128 ACAATTCATA
* * *
3138 TCACTT TCAATT CCAATT TCACTT TCACTT TCACTT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCA
3177 ATTTTGATCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.23, C:0.31, G:0.00, T:0.46
Consensus pattern (6 bp):
TCACTT
Found at i:7107 original size:6 final size:6
Alignment explanation
Indices: 7082--7120 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
7072 ACAATTCATA
* * *
7082 TCACTT TCAATT CCAATT TCACTT TCACTT TCACTT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCA
7121 ATTTTGATCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.23, C:0.31, G:0.00, T:0.46
Consensus pattern (6 bp):
TCACTT
Found at i:11581 original size:23 final size:23
Alignment explanation
Indices: 11555--11608 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
11545 CCATCCTTGC
* *
11555 TGACTAGACCTTTTGGAAGCTGT
1 TGACTAGACCTTCTAGAAGCTGT
* *
11578 TGACTGGATCTTCTAGAAGCTGT
1 TGACTAGACCTTCTAGAAGCTGT
11601 TGACTAGA
1 TGACTAGA
11609 TGTCACGTCA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (23 bp):
TGACTAGACCTTCTAGAAGCTGT
Found at i:17737 original size:23 final size:23
Alignment explanation
Indices: 17709--17766 Score: 91
Period size: 23 Copynumber: 2.5 Consensus size: 23
17699 CGTCCATCCT
*
17709 TGCTGACTAGATCTTCTGGAAGC
1 TGCTGACTAGATCTTCTAGAAGC
17732 TGCTGACT-GAATCTTCTAGAAGC
1 TGCTGACTAG-ATCTTCTAGAAGC
17755 TGCTGACTAGAT
1 TGCTGACTAGAT
17767 GCCACGTCAG
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
22 1 0.03
23 30 0.94
24 1 0.03
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.31
Consensus pattern (23 bp):
TGCTGACTAGATCTTCTAGAAGC
Found at i:18577 original size:29 final size:29
Alignment explanation
Indices: 18518--18599 Score: 87
Period size: 29 Copynumber: 2.8 Consensus size: 29
18508 AAATTTTATT
* * *
18518 TAAAGTTCATTTTAGTCCTGAAA-CTCAC
1 TAAAATTCAATTTAGTCCTTAAATCTCAC
*
18546 TAAAAATTCAATTTAGTCCTTAAATC-CTC
1 T-AAAATTCAATTTAGTCCTTAAATCTCAC
*
18575 TAAAATTACAATTTAATCCTTAAAT
1 TAAAATT-CAATTTAGTCCTTAAAT
18600 TAAAATTAAG
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
28 7 0.15
29 38 0.83
30 1 0.02
ACGTcount: A:0.39, C:0.18, G:0.05, T:0.38
Consensus pattern (29 bp):
TAAAATTCAATTTAGTCCTTAAATCTCAC
Found at i:24075 original size:23 final size:24
Alignment explanation
Indices: 24031--24078 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
24021 TTTTTTAAGT
* *
24031 TAATGGTCAAAATTAACTAAAAAA
1 TAATGATCAAAATTAACAAAAAAA
*
24055 TAATGATC-AAATTGACAAAAAAA
1 TAATGATCAAAATTAACAAAAAAA
24078 T
1 T
24079 GTAAGTATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.58, C:0.08, G:0.08, T:0.25
Consensus pattern (24 bp):
TAATGATCAAAATTAACAAAAAAA
Found at i:24121 original size:13 final size:13
Alignment explanation
Indices: 24105--24136 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
24095 AAATTTAACA
24105 TTATACTTTATTT
1 TTATACTTTATTT
24118 TTATACTTTATTT
1 TTATACTTTATTT
24131 TTATAC
1 TTATAC
24137 AAATTTAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.25, C:0.09, G:0.00, T:0.66
Consensus pattern (13 bp):
TTATACTTTATTT
Found at i:29821 original size:26 final size:25
Alignment explanation
Indices: 29751--29821 Score: 97
Period size: 25 Copynumber: 2.8 Consensus size: 25
29741 GGAGTAATAC
29751 TCTGTCTGGCTCGTAAGAGCGATAT
1 TCTGTCTGGCTCGTAAGAGCGATAT
*
29776 TCTGTCTAGCTCGTAAGAGCGATAT
1 TCTGTCTGGCTCGTAAGAGCGATAT
* * *
29801 TTTGTTTGGGCTCGTATGAGC
1 TCTGTCT-GGCTCGTAAGAGC
29822 TAAATTTCCA
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
25 29 0.73
26 11 0.28
ACGTcount: A:0.18, C:0.18, G:0.28, T:0.35
Consensus pattern (25 bp):
TCTGTCTGGCTCGTAAGAGCGATAT
Found at i:31520 original size:26 final size:26
Alignment explanation
Indices: 31491--31554 Score: 92
Period size: 26 Copynumber: 2.5 Consensus size: 26
31481 GTGTTGTCCA
***
31491 GCTCGTAAGAGCGATATTCTGTTTGC
1 GCTCGTAAGAGCGATATTCCAATTGC
*
31517 GCTCGTAAGAGCGATATTCCAATTGG
1 GCTCGTAAGAGCGATATTCCAATTGC
31543 GCTCGTAAGAGC
1 GCTCGTAAGAGC
31555 TAAACCCTGT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.28
Consensus pattern (26 bp):
GCTCGTAAGAGCGATATTCCAATTGC
Found at i:35613 original size:72 final size:72
Alignment explanation
Indices: 35481--35624 Score: 229
Period size: 72 Copynumber: 2.0 Consensus size: 72
35471 TATAGTCTGA
* * *
35481 CCCAAATTAACCTTAGAATGACAAAAATGTCCCTAAATGATAGATGACTTAAGGCTGCTTGACAT
1 CCCAAATTAACCTAAGAATGACAAAAATATCCCTAAATGATAAATGACTTAAGGCTGCTTGACAT
35546 TAAATTG
66 TAAATTG
35553 CCCAAATTAACCTAAGAATGACAAAAATATCCCTAAATGATAAATG-CTTAA-GCTTGGCTTGAC
1 CCCAAATTAACCTAAGAATGACAAAAATATCCCTAAATGATAAATGACTTAAGGC-T-GCTTGAC
35616 ATTAAATTG
64 ATTAAATTG
35625 GCCCTACAAA
Statistics
Matches: 67, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
70 2 0.03
71 6 0.09
72 59 0.88
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.28
Consensus pattern (72 bp):
CCCAAATTAACCTAAGAATGACAAAAATATCCCTAAATGATAAATGACTTAAGGCTGCTTGACAT
TAAATTG
Found at i:35680 original size:22 final size:22
Alignment explanation
Indices: 35650--35691 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
35640 ACTACTCAAG
*
35650 CTTTAGTGTTGCGACACCCAAC
1 CTTTAGTGTTGCAACACCCAAC
*
35672 CTTTTGTGTTGCAACACCCA
1 CTTTAGTGTTGCAACACCCA
35692 TGGAAGTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.21, C:0.31, G:0.17, T:0.31
Consensus pattern (22 bp):
CTTTAGTGTTGCAACACCCAAC
Found at i:37958 original size:29 final size:29
Alignment explanation
Indices: 37903--37959 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
37893 CCTTTGACCT
* *
37903 ATAAAATGCATCCAGGTCAGCATACTTTA
1 ATAAAACGCATCCAGGTCAGCACACTTTA
* *
37932 ATAAAACGCTTCCAGGTCAGCGCACTTT
1 ATAAAACGCATCCAGGTCAGCACACTTT
37960 TTGCCCGTGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.26
Consensus pattern (29 bp):
ATAAAACGCATCCAGGTCAGCACACTTTA
Found at i:46750 original size:27 final size:28
Alignment explanation
Indices: 46718--46784 Score: 100
Period size: 28 Copynumber: 2.4 Consensus size: 28
46708 TTTAACGCAA
* *
46718 ATAGCCACAAAGGCGT-CGTTGATAAAG
1 ATAGCCACAAAGGAGTCCGTTGACAAAG
*
46745 ATAGCCACAAAGGAGTCCTTTGACAAAG
1 ATAGCCACAAAGGAGTCCGTTGACAAAG
46773 ATAGCCACAAAG
1 ATAGCCACAAAG
46785 ACTTTCCCAT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
27 15 0.42
28 21 0.58
ACGTcount: A:0.40, C:0.21, G:0.22, T:0.16
Consensus pattern (28 bp):
ATAGCCACAAAGGAGTCCGTTGACAAAG
Found at i:46933 original size:29 final size:29
Alignment explanation
Indices: 46883--47064 Score: 134
Period size: 29 Copynumber: 6.6 Consensus size: 29
46873 ACAGAGACGG
*
46883 CCACGAAGGC-TC-CTTTAATAGATTCAA
1 CCACAAAGGCTTCACTTTAATAGATTCAA
*
46910 CCACAAAGGCTTCACTTTAATAGAATT-AG
1 CCACAAAGGCTTCACTTTAATAG-ATTCAA
* * *
46939 CCACAAAAGC-TCACTTTAATAGAATCAG
1 CCACAAAGGCTTCACTTTAATAGATTCAA
* * *
46967 CCATAAAGGCTTCACTTTTATAGAATCAA
1 CCACAAAGGCTTCACTTTAATAGATTCAA
* * * *
46996 CCACAAAAG-TTTAC----ATA-A-CCAG
1 CCACAAAGGCTTCACTTTAATAGATTCAA
* *
47018 TCACAAAGACTTCACTTTAATAGATTCAA
1 CCACAAAGGCTTCACTTTAATAGATTCAA
* *
47047 CCACAAATGCCTCACTTT
1 CCACAAAGGCTTCACTTT
47065 TATGGAAGCT
Statistics
Matches: 120, Mismatches: 23, Indels: 22
0.73 0.14 0.13
Matches are distributed among these distances:
22 8 0.07
23 5 0.04
24 3 0.03
27 14 0.12
28 29 0.24
29 58 0.48
30 3 0.03
ACGTcount: A:0.38, C:0.25, G:0.10, T:0.26
Consensus pattern (29 bp):
CCACAAAGGCTTCACTTTAATAGATTCAA
Found at i:46961 original size:28 final size:29
Alignment explanation
Indices: 46882--47002 Score: 149
Period size: 29 Copynumber: 4.3 Consensus size: 29
46872 AACAGAGACG
* *
46882 GCCACGAAGGC-TC-CTTTAATAGATTCA
1 GCCACAAAGGCTTCACTTTAATAGAATCA
* *
46909 ACCACAAAGGCTTCACTTTAATAGAATTA
1 GCCACAAAGGCTTCACTTTAATAGAATCA
*
46938 GCCACAAAAGC-TCACTTTAATAGAATCA
1 GCCACAAAGGCTTCACTTTAATAGAATCA
* *
46966 GCCATAAAGGCTTCACTTTTATAGAATCA
1 GCCACAAAGGCTTCACTTTAATAGAATCA
*
46995 ACCACAAA
1 GCCACAAA
47003 AGTTTACATA
Statistics
Matches: 79, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
27 9 0.11
28 27 0.34
29 43 0.54
ACGTcount: A:0.39, C:0.24, G:0.12, T:0.25
Consensus pattern (29 bp):
GCCACAAAGGCTTCACTTTAATAGAATCA
Found at i:46961 original size:57 final size:56
Alignment explanation
Indices: 46882--47004 Score: 165
Period size: 57 Copynumber: 2.2 Consensus size: 56
46872 AACAGAGACG
* * * *
46882 GCCACGAAGGCTCCTTTAATAGATTCAACCACAAAGGCTTCACTTTAATAGAATTA
1 GCCACAAAAGCTCCTTTAATAGAATCAACCACAAAGGCTTCACTTTAATAGAATCA
* * *
46938 GCCACAAAAGCTCACTTTAATAGAATCAGCCATAAAGGCTTCACTTTTATAGAATCA
1 GCCACAAAAGCTC-CTTTAATAGAATCAACCACAAAGGCTTCACTTTAATAGAATCA
*
46995 ACCACAAAAG
1 GCCACAAAAG
47005 TTTACATAAC
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
56 11 0.19
57 47 0.81
ACGTcount: A:0.39, C:0.24, G:0.13, T:0.24
Consensus pattern (56 bp):
GCCACAAAAGCTCCTTTAATAGAATCAACCACAAAGGCTTCACTTTAATAGAATCA
Found at i:47256 original size:55 final size:55
Alignment explanation
Indices: 47172--47275 Score: 172
Period size: 55 Copynumber: 1.9 Consensus size: 55
47162 CCTTTTTTTC
*
47172 ATATGATGTCATAACCACCATGACTAGGTCTTACACTCTATGATCTTCATTCCCA
1 ATATGATGTCATAACCACCATGACTAGGTCTTACACTATATGATCTTCATTCCCA
* * *
47227 ATATGATGTCATAGCCACCTTGACTAGGTCTTACACTATATGGTCTTCA
1 ATATGATGTCATAACCACCATGACTAGGTCTTACACTATATGATCTTCA
47276 ATTTCCATGG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
55 45 1.00
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.34
Consensus pattern (55 bp):
ATATGATGTCATAACCACCATGACTAGGTCTTACACTATATGATCTTCATTCCCA
Found at i:51881 original size:20 final size:21
Alignment explanation
Indices: 51848--51886 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
51838 AAGGAATGGA
*
51848 AAAAAATAGAACAGTAAAGAG
1 AAAAAATAGAACAGAAAAGAG
51869 AAAAAATAG-ACAGAAAAG
1 AAAAAATAGAACAGAAAAG
51887 CACACCAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.69, C:0.05, G:0.18, T:0.08
Consensus pattern (21 bp):
AAAAAATAGAACAGAAAAGAG
Found at i:55485 original size:21 final size:18
Alignment explanation
Indices: 55460--55502 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
55450 TCGAAAGATC
55460 ATCTTCATTC-TCCACAGG
1 ATCTTC-TTCTTCCACAGG
*
55478 ATCTTCTTCTTCCTCAGG
1 ATCTTCTTCTTCCACAGG
55496 ATCTTCT
1 ATCTTCT
55503 CCTTTAACAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 3 0.13
18 20 0.87
ACGTcount: A:0.16, C:0.33, G:0.09, T:0.42
Consensus pattern (18 bp):
ATCTTCTTCTTCCACAGG
Found at i:57047 original size:106 final size:105
Alignment explanation
Indices: 56932--57134 Score: 329
Period size: 106 Copynumber: 1.9 Consensus size: 105
56922 ATATTAAAAC
* *
56932 AAATCTTAATTCAAACTTTTGATAA-ATATTAATATAAATTATAAAATTTAATTTATAATTAATA
1 AAATCTTAATTCAAACTCTAGATAATA-ATTAATATAAATTATAAAATTTAATTTATAATTAATA
*
56996 TTAAGAGTTA-TCAAAATTTTGAAAAAATAAAAATTTAATGAA
65 TTAAGAATTATTCAAAA-TTTG-AAAAATAAAAATTTAATGAA
57038 AAATCTTAATTCAAACTCTAGATAATAATTAATATAAATTATAAAATTTAATTTATAATTAATAT
1 AAATCTTAATTCAAACTCTAGATAATAATTAATATAAATTATAAAATTTAATTTATAATTAATAT
*
57103 TAATAATTATTCAAAATTTGAAAAATAAAAAT
66 TAAGAATTATTCAAAATTTGAAAAATAAAAAT
57135 AAAATAAAAT
Statistics
Matches: 91, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
105 12 0.13
106 72 0.79
107 7 0.08
ACGTcount: A:0.53, C:0.04, G:0.03, T:0.39
Consensus pattern (105 bp):
AAATCTTAATTCAAACTCTAGATAATAATTAATATAAATTATAAAATTTAATTTATAATTAATAT
TAAGAATTATTCAAAATTTGAAAAATAAAAATTTAATGAA
Found at i:57212 original size:150 final size:153
Alignment explanation
Indices: 57038--57317 Score: 446
Period size: 150 Copynumber: 1.8 Consensus size: 153
57028 ATTTAATGAA
*
57038 AAATCTTAATTCAAACTCTAGATAATAATTAATATAAATTATAAAATTTAATTTATAA-TTAATA
1 AAATATTAATTCAAACTCTAGATAATAATTAATATAAATTATAAAATTTAATTTATAATTTAATA
* *
57102 TTAATAATTATTCAAAA-TTTGAAAAA-TAAAAATAAAATA-A-AATTTAAATGAAAAA-CTTTA
66 TTAAGAATTA-TCAAAATTTTGAAAAAGT--AAATAAAATAGATAATTTAAATAAAAAACCTTTA
57162 TTTAAATTTAAAATTTTAAAGAAAAC
128 TTTAAATTTAAAATTTTAAAGAAAAC
*
57188 AAATATTAATTCAAACTCTTGATAATAATTAATATAAATTATAAAATTTAATTTATAATTTAATA
1 AAATATTAATTCAAACTCTAGATAATAATTAATATAAATTATAAAATTTAATTTATAATTTAATA
*
57253 TTAAGAATTATCAAAATTTTGAAAAAGTAAATAAAATAGATGATTTAAATAAAAAACCTTTATTT
66 TTAAGAATTATCAAAATTTTGAAAAAGTAAATAAAATAGATAATTTAAATAAAAAACCTTTATTT
57318 TTAGTTGTTT
Statistics
Matches: 119, Mismatches: 5, Indels: 9
0.89 0.04 0.07
Matches are distributed among these distances:
150 72 0.61
151 25 0.21
152 14 0.12
153 8 0.07
ACGTcount: A:0.54, C:0.05, G:0.04, T:0.38
Consensus pattern (153 bp):
AAATATTAATTCAAACTCTAGATAATAATTAATATAAATTATAAAATTTAATTTATAATTTAATA
TTAAGAATTATCAAAATTTTGAAAAAGTAAATAAAATAGATAATTTAAATAAAAAACCTTTATTT
AAATTTAAAATTTTAAAGAAAAC
Found at i:57231 original size:19 final size:20
Alignment explanation
Indices: 57209--57256 Score: 50
Period size: 19 Copynumber: 2.5 Consensus size: 20
57199 CAAACTCTTG
57209 ATAATAATTAATATA-AATT
1 ATAATAATTAATATATAATT
*
57228 ATAA-AATTTAATTTATAATT
1 ATAATAA-TTAATATATAATT
57248 -TAAT-ATTAA
1 ATAATAATTAA
57257 GAATTATCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
18 6 0.24
19 15 0.60
20 4 0.16
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
ATAATAATTAATATATAATT
Found at i:77119 original size:15 final size:12
Alignment explanation
Indices: 77085--77109 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
77075 CGGTAGGCTC
77085 TTCTTCTTCCTT
1 TTCTTCTTCCTT
77097 TTCTTCTTCCTT
1 TTCTTCTTCCTT
77109 T
1 T
77110 CCCTCTTCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (12 bp):
TTCTTCTTCCTT
Found at i:84655 original size:17 final size:17
Alignment explanation
Indices: 84624--84656 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
84614 AAATAACAAC
84624 AGTTAGTAAAGATTAAA
1 AGTTAGTAAAGATTAAA
84641 AGTTAAGTAAA-ATTAA
1 AGTT-AGTAAAGATTAA
84657 TTGCAACTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.55, C:0.00, G:0.15, T:0.30
Consensus pattern (17 bp):
AGTTAGTAAAGATTAAA
Found at i:90843 original size:23 final size:23
Alignment explanation
Indices: 90783--90868 Score: 82
Period size: 23 Copynumber: 3.7 Consensus size: 23
90773 ATTTTCACCC
* * *
90783 AAGTGCCACTATCAAGTGCACCG
1 AAGTGCCACTTTCAATTGCATCG
* * * *
90806 TACTACCACTGTCAATTGCATCG
1 AAGTGCCACTTTCAATTGCATCG
* *
90829 AAGTGCTACTTTCAATTGCATTG
1 AAGTGCCACTTTCAATTGCATCG
*
90852 AAGTGCCACTTTTAATT
1 AAGTGCCACTTTCAATT
90869 TGCGCGCTAA
Statistics
Matches: 49, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 49 1.00
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.31
Consensus pattern (23 bp):
AAGTGCCACTTTCAATTGCATCG
Found at i:92265 original size:108 final size:108
Alignment explanation
Indices: 92068--92282 Score: 299
Period size: 108 Copynumber: 2.0 Consensus size: 108
92058 TCATCAAAAA
* *
92068 GAACATTATTGATTTAAAATAGGATACTCAATTATTTAGGTTCAGAGAAAAAAAAATACCCAGTA
1 GAACATTATTGATTTAAAATAGGATACTCAACTATTTAGGTTCAAAGAAAAAAAAATACCCAGTA
* * *
92133 CGTTTGAGTATAATTTCTCGAATTCCCTAAATAAAAGAACATC
66 CGTTTGAGCACAATTTCTCAAATTCCCTAAATAAAAGAACATC
* * **
92176 GAACATTTATTGATGTT-AAATAGGATACTCGACTATTTATGTTCAAAG-AAAAATTATACCCAG
1 GAACA-TTATTGAT-TTAAAATAGGATACTCAACTATTTAGGTTCAAAGAAAAAAAAATACCCAG
* *
92239 TACGTTTGAGCACAATTTTTTAAATTCCCTAAATAAAAGAACAT
64 TACGTTTGAGCACAATTTCTCAAATTCCCTAAATAAAAGAACAT
92283 TGTCTTTTTT
Statistics
Matches: 94, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
108 57 0.61
109 35 0.37
110 2 0.02
ACGTcount: A:0.41, C:0.14, G:0.13, T:0.32
Consensus pattern (108 bp):
GAACATTATTGATTTAAAATAGGATACTCAACTATTTAGGTTCAAAGAAAAAAAAATACCCAGTA
CGTTTGAGCACAATTTCTCAAATTCCCTAAATAAAAGAACATC
Found at i:92867 original size:22 final size:24
Alignment explanation
Indices: 92824--92868 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
92814 TTAAAATAAA
* *
92824 TAAAAAAGACTAAAATGACAGAAT
1 TAAAAAACACTAAAACGACAGAAT
92848 TAAAAAACA-TAAAACG-CAGAA
1 TAAAAAACACTAAAACGACAGAA
92869 GGATCAAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 5 0.26
23 6 0.32
24 8 0.42
ACGTcount: A:0.64, C:0.11, G:0.11, T:0.13
Consensus pattern (24 bp):
TAAAAAACACTAAAACGACAGAAT
Found at i:93910 original size:14 final size:15
Alignment explanation
Indices: 93860--93911 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 15
93850 GGGTCAAGTG
*
93860 TTTGGGTTT-GGTAG
1 TTTGGGTTTGGGTAT
*
93874 TTTGGTTTTGGGTAT
1 TTTGGGTTTGGGTAT
93889 AATTTGGGTTTGGGT-T
1 --TTTGGGTTTGGGTAT
93905 TTTGGGT
1 TTTGGGT
93912 ATTTTTAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
14 15 0.47
15 4 0.12
16 1 0.03
17 12 0.38
ACGTcount: A:0.08, C:0.00, G:0.38, T:0.54
Consensus pattern (15 bp):
TTTGGGTTTGGGTAT
Found at i:94334 original size:42 final size:43
Alignment explanation
Indices: 94297--94991 Score: 724
Period size: 43 Copynumber: 16.3 Consensus size: 43
94287 GCCCCTCTAA
* * * * **
94297 ATTAGGGGTAAAAGACTAGATGACTTCAATCTACCCCT-CTAT
1 ATTAGGGGTAAAAGATTGGATGGCTTCAATCTGCCCCTACTGG
*
94339 ATTAGGGGTAAAAGATTGGATGGCTTTAATCTGCCCCTACTGG
1 ATTAGGGGTAAAAGATTGGATGGCTTCAATCTGCCCCTACTGG
* * **
94382 ATTAAGGGTAAAAGATTGGATGGCTTCAATCTG-CCTTTTTGG
1 ATTAGGGGTAAAAGATTGGATGGCTTCAATCTGCCCCTACTGG
* * * * *
94424 ATTAGTGGTAAAAGACTGGATGGCTTTAATCTGCCTCT-TTGG
1 ATTAGGGGTAAAAGATTGGATGGCTTCAATCTGCCCCTACTGG
* * *
94466 ATTAGTGGTAAAAGACTGGATGGTTTCAATCTGCCCCTACTGG
1 ATTAGGGGTAAAAGATTGGATGGCTTCAATCTGCCCCTACTGG
** * *
94509 ATTAGGGGTAAAAGATTGGATGATTTCAATCTGCCCCT-TTGA
1 ATTAGGGGTAAAAGATTGGATGGCTTCAATCTGCCCCTACTGG
* * * * * *
94551 ATTAAGGGTAAAAGACTGAATGGTTTCAATCTGCCCTTATTGG
1 ATTAGGGGTAAAAGATTGGATGGCTTCAATCTGCCCCTACTGG
* * * * *
94594 ATTAGGGGTAAAAGATTGGATGACTTTAATCTGCCCTTATTAG
1 ATTAGGGGTAAAAGATTGGATGGCTTCAATCTGCCCCTACTGG
* * * * *
94637 ATTAGGGTTAAAAGATTAGATGGCTTCAATCTG-GCTTACTAG
1 ATTAGGGGTAAAAGATTGGATGGCTTCAATCTGCCCCTACTGG
* * *
94679 ATTAAGGGTAAAAGATTGGATGGCTTCAATCTGCCCTTATTGG
1 ATTAGGGGTAAAAGATTGGATGGCTTCAATCTGCCCCTACTGG
* * * *
94722 ATTAAGGGTAAAAGATTAGG-TAGCTTCAATCTGCCCC-ATTGA
1 ATTAGGGGTAAAAGATT-GGATGGCTTCAATCTGCCCCTACTGG
* *
94764 ATTAGGGGTAAAAGATTAGATGGCTTCAATCTGCCCCTACTAG
1 ATTAGGGGTAAAAGATTGGATGGCTTCAATCTGCCCCTACTGG
* * * *
94807 ATTAGGGGTAAAAGATTGGATGGTTTCAATTTGCTCATACTGG
1 ATTAGGGGTAAAAGATTGGATGGCTTCAATCTGCCCCTACTGG
* * * ** *
94850 ATTAGGGATAAAAGATTGGATGACTTTAATCTGCCTTTACTAG
1 ATTAGGGGTAAAAGATTGGATGGCTTCAATCTGCCCCTACTGG
* * * *
94893 ATTAGGGGTAAAAGACTAGATGACTTCAATCTGCCCCTATTGG
1 ATTAGGGGTAAAAGATTGGATGGCTTCAATCTGCCCCTACTGG
* * * *
94936 ATTTGAGGT--AAGACTGGATGGCTTCAATCTACCCCTACTGG
1 ATTAGGGGTAAAAGATTGGATGGCTTCAATCTGCCCCTACTGG
94977 ATTAGGGGTAAAAGA
1 ATTAGGGGTAAAAGA
94992 CAGGATGGTG
Statistics
Matches: 551, Mismatches: 92, Indels: 19
0.83 0.14 0.03
Matches are distributed among these distances:
41 36 0.07
42 215 0.39
43 298 0.54
44 2 0.00
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.32
Consensus pattern (43 bp):
ATTAGGGGTAAAAGATTGGATGGCTTCAATCTGCCCCTACTGG
Found at i:94445 original size:85 final size:85
Alignment explanation
Indices: 94339--94991 Score: 692
Period size: 85 Copynumber: 7.7 Consensus size: 85
94329 ACCCCTCTAT
94339 ATTAGGGGTAAAAGATTGGATGGCTTTAATCTGCCCCTACTGGATTAAGGGTAAAAGATTGGATG
1 ATTAGGGGTAAAAGATTGGATGGCTTTAATCTGCCCCTACTGGATTAAGGGTAAAAGATTGGATG
* *
94404 GCTTCAATCTGCCTTTTTGG
66 GCTTCAATCTGCCCTATTGG
* * * * *
94424 ATTAGTGGTAAAAGACTGGATGGCTTTAATCTGCCTCT-TTGGATT-AGTGGTAAAAGACTGGAT
1 ATTAGGGGTAAAAGATTGGATGGCTTTAATCTGCCCCTACTGGATTAAG-GGTAAAAGATTGGAT
* *
94487 GGTTTCAATCTGCCCCTACTGG
65 GGCTTCAATCTG-CCCTATTGG
* * * * *
94509 ATTAGGGGTAAAAGATTGGAT-GATTTCAATCTGCCCCT-TTGAATTAAGGGTAAAAGACTGAAT
1 ATTAGGGGTAAAAGATTGGATGGCTTT-AATCTGCCCCTACTGGATTAAGGGTAAAAGATTGGAT
*
94572 GGTTTCAATCTGCCCTTATTGG
65 GGCTTCAATCTGCCC-TATTGG
* * * * *
94594 ATTAGGGGTAAAAGATTGGATGACTTTAATCTGCCCTTATTAGATT-AGGGTTAAAAGATTAGAT
1 ATTAGGGGTAAAAGATTGGATGGCTTTAATCTGCCCCTACTGGATTAAGGG-TAAAAGATTGGAT
* * * *
94658 GGCTTCAATCTGGCTTACTAG
65 GGCTTCAATCTGCCCTATTGG
* * * *
94679 ATTAAGGGTAAAAGATTGGATGGCTTCAATCTGCCCTTATTGGATTAAGGGTAAAAGATTAGG-T
1 ATTAGGGGTAAAAGATTGGATGGCTTTAATCTGCCCCTACTGGATTAAGGGTAAAAGATT-GGAT
* * *
94743 AGCTTCAATCTGCCCCATTGA
65 GGCTTCAATCTGCCCTATTGG
* * * *
94764 ATTAGGGGTAAAAGATTAGATGGCTTCAATCTGCCCCTACTAGATTAGGGGTAAAAGATTGGATG
1 ATTAGGGGTAAAAGATTGGATGGCTTTAATCTGCCCCTACTGGATTAAGGGTAAAAGATTGGATG
* * * *
94829 GTTTCAATTTGCTCATACTGG
66 GCTTCAATCTGC-CCTATTGG
* * ** * * * *
94850 ATTAGGGATAAAAGATTGGATGACTTTAATCTGCCTTTACTAGATTAGGGGTAAAAGACTAGATG
1 ATTAGGGGTAAAAGATTGGATGGCTTTAATCTGCCCCTACTGGATTAAGGGTAAAAGATTGGATG
*
94915 ACTTCAATCTGCCCCTATTGG
66 GCTTCAATCTG-CCCTATTGG
* * * * * *
94936 ATTTGAGGT--AAGACTGGATGGCTTCAATCTACCCCTACTGGATTAGGGGTAAAAGA
1 ATTAGGGGTAAAAGATTGGATGGCTTTAATCTGCCCCTACTGGATTAAGGGTAAAAGA
94992 CAGGATGGTG
Statistics
Matches: 478, Mismatches: 77, Indels: 27
0.82 0.13 0.05
Matches are distributed among these distances:
83 2 0.00
84 80 0.17
85 277 0.58
86 118 0.25
87 1 0.00
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.32
Consensus pattern (85 bp):
ATTAGGGGTAAAAGATTGGATGGCTTTAATCTGCCCCTACTGGATTAAGGGTAAAAGATTGGATG
GCTTCAATCTGCCCTATTGG
Found at i:94528 original size:170 final size:172
Alignment explanation
Indices: 94278--95000 Score: 795
Period size: 170 Copynumber: 4.3 Consensus size: 172
94268 GTGTGTGTGA
* * ** * *
94278 CTTCAA-CTTGCCCCT-CTAAATTAGGGGTAAAAGACTAGATGACTTCAATCTACCCCT-CTATA
1 CTTCAATC-TGCCCCTACTAGATTAGGGGTAAAAGACTGGATGGTTTCAATCTGCCCCTACTAGA
*
94340 TTAGGGGTAAAAGATTGGATGGCTTTAATCTGCCCCTACTGGATTAAGGGTAAAAGATTGGATGG
65 TTAGGGGTAAAAGATTGGATGGCTTTAATCTGCCCCTACTGGATTAAGGGTAAAAGACTGGATGG
* * *
94405 CTTCAATCTG-CCTTTTTGGATTAGTGGTAAAAGACTGGATGG
130 CTTCAATCTGCCCCTATTGGATTAGGGGTAAAAGACTGGATGG
* * * * * *
94447 CTTTAATCTGCCTCT-TTGGATTAGTGGTAAAAGACTGGATGGTTTCAATCTGCCCCTACTGGAT
1 CTTCAATCTGCCCCTACTAGATTAGGGGTAAAAGACTGGATGGTTTCAATCTGCCCCTACTAGAT
* * * *
94511 TAGGGGTAAAAGATTGGAT-GATTTCAATCTGCCCCT-TTGAATTAAGGGTAAAAGACTGAATGG
66 TAGGGGTAAAAGATTGGATGGCTTT-AATCTGCCCCTACTGGATTAAGGGTAAAAGACTGGATGG
* * * *
94574 TTTCAATCTGCCCTTATTGGATTAGGGGTAAAAGATTGGATGA
130 CTTCAATCTGCCCCTATTGGATTAGGGGTAAAAGACTGGATGG
* * * * * * * * *
94617 CTTTAATCTGCCCTTATTAGATTAGGGTTAAAAGATTAGATGGCTTCAATCTG-GCTTACTAGAT
1 CTTCAATCTGCCCCTACTAGATTAGGGGTAAAAGACTGGATGGTTTCAATCTGCCCCTACTAGAT
* * * * * *
94681 TAAGGGTAAAAGATTGGATGGCTTCAATCTGCCCTTATTGGATTAAGGGTAAAAGATTAGG-TAG
66 TAGGGGTAAAAGATTGGATGGCTTTAATCTGCCCCTACTGGATTAAGGGTAAAAGACT-GGATGG
* * *
94745 CTTCAATCTGCCCC-ATTGAATTAGGGGTAAAAGATTAGATGG
130 CTTCAATCTGCCCCTATTGGATTAGGGGTAAAAGACTGGATGG
* * * * *
94787 CTTCAATCTGCCCCTACTAGATTAGGGGTAAAAGATTGGATGGTTTCAATTTGCTCATACTGGAT
1 CTTCAATCTGCCCCTACTAGATTAGGGGTAAAAGACTGGATGGTTTCAATCTGCCCCTACTAGAT
* * ** * * * *
94852 TAGGGATAAAAGATTGGATGACTTTAATCTGCCTTTACTAGATTAGGGGTAAAAGACTAGATGAC
66 TAGGGGTAAAAGATTGGATGGCTTTAATCTGCCCCTACTGGATTAAGGGTAAAAGACTGGATGGC
* *
94917 TTCAATCTGCCCCTATTGGATTTGAGGT--AAGACTGGATGG
131 TTCAATCTGCCCCTATTGGATTAGGGGTAAAAGACTGGATGG
* * *
94957 CTTCAATCTACCCCTACTGGATTAGGGGTAAAAGACAGGATGGT
1 CTTCAATCTGCCCCTACTAGATTAGGGGTAAAAGACTGGATGGT
95001 GATGTAACTT
Statistics
Matches: 466, Mismatches: 77, Indels: 21
0.83 0.14 0.04
Matches are distributed among these distances:
169 81 0.17
170 234 0.50
171 139 0.30
172 12 0.03
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.32
Consensus pattern (172 bp):
CTTCAATCTGCCCCTACTAGATTAGGGGTAAAAGACTGGATGGTTTCAATCTGCCCCTACTAGAT
TAGGGGTAAAAGATTGGATGGCTTTAATCTGCCCCTACTGGATTAAGGGTAAAAGACTGGATGGC
TTCAATCTGCCCCTATTGGATTAGGGGTAAAAGACTGGATGG
Found at i:96012 original size:7 final size:7
Alignment explanation
Indices: 96000--96080 Score: 62
Period size: 7 Copynumber: 11.4 Consensus size: 7
95990 TCTCCTTTGC
96000 TTTCTTT
1 TTTCTTT
96007 TTTC-TT
1 TTTCTTT
96013 TTTCTTT
1 TTTCTTT
*
96020 TCATCCTTT
1 T--TTCTTT
96029 TTCTCTTT
1 TT-TCTTT
96037 TTTCTTT
1 TTTCTTT
96044 TTTC---
1 TTTCTTT
96048 TTTCTTT
1 TTTCTTT
*
96055 TTCCTTT
1 TTTCTTT
*
96062 TTCTTTTCT
1 TT-TCTT-T
96071 TTTCTTT
1 TTTCTTT
96078 TTT
1 TTT
96081 TTTGGTGAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 18
0.71 0.07 0.22
Matches are distributed among these distances:
4 4 0.07
6 6 0.10
7 29 0.49
8 11 0.19
9 9 0.15
ACGTcount: A:0.01, C:0.20, G:0.00, T:0.79
Consensus pattern (7 bp):
TTTCTTT
Found at i:96027 original size:31 final size:31
Alignment explanation
Indices: 96002--96080 Score: 97
Period size: 33 Copynumber: 2.5 Consensus size: 31
95992 TCCTTTGCTT
96002 TCTTTTTTC-TTTTTCTTTTCATCCTTTTTC
1 TCTTTTTTCTTTTTTCTTTTCATCCTTTTTC
**
96032 TCTTTTTTCTTTTTTCTTTCTTTTTCCTTTTTC
1 TCTTTTTTCTTTTTTC-TT-TTCATCCTTTTTC
*
96065 TTTTCTTTTCTTTTTT
1 TCTT-TTTTCTTTTTT
96081 TTTGGTGAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
30 9 0.21
31 6 0.14
32 2 0.05
33 14 0.33
34 11 0.26
ACGTcount: A:0.01, C:0.20, G:0.00, T:0.78
Consensus pattern (31 bp):
TCTTTTTTCTTTTTTCTTTTCATCCTTTTTC
Found at i:96043 original size:24 final size:23
Alignment explanation
Indices: 96003--96069 Score: 75
Period size: 26 Copynumber: 2.9 Consensus size: 23
95993 CCTTTGCTTT
96003 CTTTTT-TCTTTTTCTTTTCATC
1 CTTTTTCTCTTTTTCTTTTCATC
* *
96025 CTTTTTCTCTTTTTTCTTTTTTCTTT
1 CTTTTTCTC-TTTTTC--TTTTCATC
96051 CTTTTTC-CTTTTTCTTTTC
1 CTTTTTCTCTTTTTCTTTTC
96070 TTTTCTTTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
22 11 0.28
23 2 0.05
24 12 0.31
25 1 0.03
26 13 0.33
ACGTcount: A:0.01, C:0.22, G:0.00, T:0.76
Consensus pattern (23 bp):
CTTTTTCTCTTTTTCTTTTCATC
Found at i:96046 original size:17 final size:17
Alignment explanation
Indices: 96000--96080 Score: 83
Period size: 17 Copynumber: 4.6 Consensus size: 17
95990 TCTCCTTTGC
96000 TTTCTTTTTTCTTTTTCT
1 TTTCTTTTTTCTTTTT-T
*
96018 TTTCATCCTTTTTC-TCTTT
1 TTTC-T--TTTTTCTTTTTT
*
96037 TTTCTTTTTTCTTTCTT
1 TTTCTTTTTTCTTTTTT
* *
96054 TTTCCTTTTTCTTTTCT
1 TTTCTTTTTTCTTTTTT
96071 TTTCTTTTTT
1 TTTCTTTTTT
96081 TTTGGTGAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
16 6 0.12
17 26 0.50
18 5 0.10
19 6 0.12
20 3 0.06
21 6 0.12
ACGTcount: A:0.01, C:0.20, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTCTTTTTTCTTTTTT
Found at i:102308 original size:24 final size:20
Alignment explanation
Indices: 102258--102299 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
102248 TTAAGTCTTC
102258 GAAAATATAAAACATTTATT
1 GAAAATATAAAACATTTATT
102278 GAAAATATAAAACATTTATT
1 GAAAATATAAAACATTTATT
102298 GA
1 GA
102300 TTTAAAATAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.55, C:0.05, G:0.07, T:0.33
Consensus pattern (20 bp):
GAAAATATAAAACATTTATT
Found at i:102430 original size:108 final size:109
Alignment explanation
Indices: 102287--102502 Score: 357
Period size: 108 Copynumber: 2.0 Consensus size: 109
102277 TGAAAATATA
*
102287 AAACATTTATTGATTTAAAATAGGATACTCGATTATTTAGGTTCAAAGAAAAAAATCAT-ACCTA
1 AAACATTTATTGATTTAAAATAGGATACTCGATTATTTAGGTTCAAAG-AAAAAATCATAATC-A
*
102351 GTA-ATTTGAGCACAATTTCTCGAATTCCCTAAATAAAAGAACATC
64 GTACATTTGAACACAATTTCTCGAATTCCCTAAATAAAAGAACATC
102396 AAACATTTATTGATTT-AAATAGGATACTCGATTATTTAGGTTCAAAGAAAAAATCATAATCAGT
1 AAACATTTATTGATTTAAAATAGGATACTCGATTATTTAGGTTCAAAGAAAAAATCATAATCAGT
* *
102460 ACATTTGAACATAATTTCTCGAATTCCCTAAATGAAAGAACAT
66 ACATTTGAACACAATTTCTCGAATTCCCTAAATAAAAGAACAT
102503 TGTTGTTTTT
Statistics
Matches: 101, Mismatches: 4, Indels: 5
0.92 0.04 0.05
Matches are distributed among these distances:
107 14 0.14
108 71 0.70
109 16 0.16
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (109 bp):
AAACATTTATTGATTTAAAATAGGATACTCGATTATTTAGGTTCAAAGAAAAAATCATAATCAGT
ACATTTGAACACAATTTCTCGAATTCCCTAAATAAAAGAACATC
Found at i:102820 original size:37 final size:35
Alignment explanation
Indices: 102779--102848 Score: 104
Period size: 35 Copynumber: 1.9 Consensus size: 35
102769 AAATACATAA
*
102779 AATAAAAGGGGAAGATTTTAGAAAAAAAAAAAAAAAG
1 AATAAAAGGGCAA-ATTTTA-AAAAAAAAAAAAAAAG
*
102816 AATAAAAGGGCAAATTTTAAAAAAAGAAAAAAA
1 AATAAAAGGGCAAATTTTAAAAAAAAAAAAAAA
102849 TTGAGGGTCG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
35 13 0.42
36 6 0.19
37 12 0.39
ACGTcount: A:0.69, C:0.01, G:0.16, T:0.14
Consensus pattern (35 bp):
AATAAAAGGGCAAATTTTAAAAAAAAAAAAAAAAG
Found at i:102840 original size:36 final size:37
Alignment explanation
Indices: 102779--102848 Score: 106
Period size: 36 Copynumber: 1.9 Consensus size: 37
102769 AAATACATAA
* *
102779 AATAAAAGGGGAAGATTTTAGAAAAAAAAAAAAAAAG
1 AATAAAAGGGCAAGATTTTAAAAAAAAAAAAAAAAAG
*
102816 AATAAAAGGGCAA-ATTTTAAAAAAAGAAAAAAA
1 AATAAAAGGGCAAGATTTTAAAAAAAAAAAAAAA
102849 TTGAGGGTCG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
36 18 0.60
37 12 0.40
ACGTcount: A:0.69, C:0.01, G:0.16, T:0.14
Consensus pattern (37 bp):
AATAAAAGGGCAAGATTTTAAAAAAAAAAAAAAAAAG
Found at i:104075 original size:6 final size:6
Alignment explanation
Indices: 104066--104172 Score: 74
Period size: 6 Copynumber: 17.3 Consensus size: 6
104056 GTTGAGCTTA
* ** ** *
104066 TTGGGT TT-GGT TTGAGT TTGGGT CTTAGGGT TTGTAT TTGGGT CAAGTGT
1 TTGGGT TTGGGT TTGGGT TTGGGT -TT-GGGT TTGGGT TTGGGT -TTGGGT
* * *
104116 TTGGGT TTGGTGGT TTGGTT TTGGGT AT-AGT TTGGGT TTGGGT TTGGGT
1 TTGGGT TT-G-GGT TTGGGT TTGGGT TTGGGT TTGGGT TTGGGT TTGGGT
104165 TTGGGT TT
1 TTGGGT TT
104173 TGTGAATGGG
Statistics
Matches: 76, Mismatches: 18, Indels: 14
0.70 0.17 0.13
Matches are distributed among these distances:
5 8 0.11
6 50 0.66
7 9 0.12
8 9 0.12
ACGTcount: A:0.07, C:0.02, G:0.41, T:0.50
Consensus pattern (6 bp):
TTGGGT
Found at i:104131 original size:33 final size:30
Alignment explanation
Indices: 104080--104170 Score: 89
Period size: 33 Copynumber: 2.9 Consensus size: 30
104070 GTTTGGTTTG
*
104080 AGTTTGGGTCTTAGGGTTT-GTATTTGGGTCA-
1 AGTTTGGGT-TTGGGGTTTGGT-TTTGGGT-AT
104111 AGTGTTTGGGTTTGGTGGTTTGGTTTTGGGTAT
1 A--GTTTGGGTTTGG-GGTTTGGTTTTGGGTAT
*
104144 AGTTTGGGTTT-GGGTTTGGGTTTGGGT
1 AGTTTGGGTTTGGGGTTTGGTTTTGGGT
104171 TTTGTGAATG
Statistics
Matches: 53, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
29 14 0.26
30 1 0.02
31 11 0.21
32 4 0.08
33 21 0.40
34 2 0.04
ACGTcount: A:0.08, C:0.02, G:0.42, T:0.48
Consensus pattern (30 bp):
AGTTTGGGTTTGGGGTTTGGTTTTGGGTAT
Found at i:104828 original size:21 final size:20
Alignment explanation
Indices: 104804--104852 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
104794 TTAAAAATAT
104804 AAAAATTAGAAAAA-GAATAGA
1 AAAAATTAGAAAAATG-ATA-A
* *
104825 AAAAACTATAAAAATGATAA
1 AAAAATTAGAAAAATGATAA
104845 AAAAATTA
1 AAAAATTA
104853 TAAATTTTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 8 0.33
21 15 0.62
22 1 0.04
ACGTcount: A:0.71, C:0.02, G:0.08, T:0.18
Consensus pattern (20 bp):
AAAAATTAGAAAAATGATAA
Found at i:105199 original size:19 final size:20
Alignment explanation
Indices: 105177--105225 Score: 73
Period size: 21 Copynumber: 2.5 Consensus size: 20
105167 TTTTTTTATG
105177 ATTTTTATAAA-ATTTTACA
1 ATTTTTATAAATATTTTACA
*
105196 ATTTTTATAAATTTTTTTACA
1 ATTTTTATAAA-TATTTTACA
105217 ATTTTTATA
1 ATTTTTATA
105226 TTTTTTTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 11 0.41
21 16 0.59
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (20 bp):
ATTTTTATAAATATTTTACA
Found at i:105228 original size:19 final size:19
Alignment explanation
Indices: 105161--105252 Score: 89
Period size: 19 Copynumber: 4.8 Consensus size: 19
105151 TTTCTATATA
**
105161 TTTT-TATTTTTTTATGAT
1 TTTTATATTTTTTTACAAT
***
105179 TTTTATAAAATTTTACAAT
1 TTTTATATTTTTTTACAAT
105198 TTTTATAAATTTTTTTACAAT
1 TTTTAT--ATTTTTTTACAAT
105219 TTTTATATTTTTTTA-AAT
1 TTTTATATTTTTTTACAAT
*
105237 TTTTAATATTTATTTA
1 TTTT-ATATTTTTTTA
105253 TTAAAATTTG
Statistics
Matches: 61, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
18 11 0.18
19 34 0.56
21 16 0.26
ACGTcount: A:0.30, C:0.02, G:0.01, T:0.66
Consensus pattern (19 bp):
TTTTATATTTTTTTACAAT
Found at i:109265 original size:53 final size:53
Alignment explanation
Indices: 109207--109312 Score: 176
Period size: 53 Copynumber: 2.0 Consensus size: 53
109197 AAGTTAGTAC
* * * *
109207 AGAAGTTTAGAATAGAGTAACTTCTTCACCATAATATTCTATTGCCAAAAATA
1 AGAAGTTCAAAATAGAGTAACTTCTTCACCACAATATTCTATTACCAAAAATA
109260 AGAAGTTCAAAATAGAGTAACTTCTTCACCACAATATTCTATTACCAAAAATA
1 AGAAGTTCAAAATAGAGTAACTTCTTCACCACAATATTCTATTACCAAAAATA
109313 GACCTAGAAG
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
53 49 1.00
ACGTcount: A:0.43, C:0.17, G:0.09, T:0.30
Consensus pattern (53 bp):
AGAAGTTCAAAATAGAGTAACTTCTTCACCACAATATTCTATTACCAAAAATA
Found at i:110289 original size:17 final size:17
Alignment explanation
Indices: 110267--110305 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
110257 AGGTGGAGAA
*
110267 CTTGTTCGTTA-AGAGTT
1 CTTGTTCG-TAGAGAATT
110284 CTTGTTCGTAGAGAATT
1 CTTGTTCGTAGAGAATT
110301 CTTGT
1 CTTGT
110306 CAAGGTGGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 2 0.10
17 18 0.90
ACGTcount: A:0.18, C:0.13, G:0.23, T:0.46
Consensus pattern (17 bp):
CTTGTTCGTAGAGAATT
Found at i:111400 original size:20 final size:20
Alignment explanation
Indices: 111377--111417 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
111367 TTTCGAGGCC
111377 AAAATTTCTTTTATGAGGGG
1 AAAATTTCTTTTATGAGGGG
111397 AAAATTTCTTTTATGAGGGG
1 AAAATTTCTTTTATGAGGGG
111417 A
1 A
111418 TTAAATTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.32, C:0.05, G:0.24, T:0.39
Consensus pattern (20 bp):
AAAATTTCTTTTATGAGGGG
Found at i:117971 original size:2 final size:2
Alignment explanation
Indices: 117964--117998 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
117954 GGAGTAATCA
*
117964 AG AG AG AG AG AG AG AA AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
117999 TGTGTGTACA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (2 bp):
AG
Found at i:121924 original size:2 final size:2
Alignment explanation
Indices: 121919--121958 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
121909 TTTAATTTAA
121919 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
121959 TGTTTTATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:123831 original size:12 final size:12
Alignment explanation
Indices: 123814--123838 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
123804 TTAAAATGAC
123814 AAAAAATAAAAT
1 AAAAAATAAAAT
123826 AAAAAATAAAAT
1 AAAAAATAAAAT
123838 A
1 A
123839 CATACATAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (12 bp):
AAAAAATAAAAT
Found at i:124528 original size:97 final size:97
Alignment explanation
Indices: 124343--124525 Score: 271
Period size: 97 Copynumber: 1.9 Consensus size: 97
124333 AAGGGTATTC
***
124343 GATTATCCCGATTTGAAGAAAAATCGTGTCTAGTAAGTTAAGGCACAAAATTTCAAAACCAGAAA
1 GATTATCCCGATTTGAAGAAAAATCGCACCTAGTAAGTTAAGGCACAAAATTTCAAAACCAGAAA
* *
124408 TAAAGTAATATTGCATTGATTTAAGAGTATCA
66 TAAAGGAATATTGCATCGATTTAAGAGTATCA
* *
124440 GATTATCCC-AGTTTGAAGAAAAATCGCACCTAGTAAGTTAAGGCACAAATTTTCAAAACCCGAA
1 GATTATCCCGA-TTTGAAGAAAAATCGCACCTAGTAAGTTAAGGCACAAAATTTCAAAACCAGAA
*
124504 A-AAAGGAATATTGCCTCGATTT
65 ATAAAGGAATATTGCATCGATTT
124526 TAAATATTTT
Statistics
Matches: 77, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
96 19 0.25
97 58 0.75
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.27
Consensus pattern (97 bp):
GATTATCCCGATTTGAAGAAAAATCGCACCTAGTAAGTTAAGGCACAAAATTTCAAAACCAGAAA
TAAAGGAATATTGCATCGATTTAAGAGTATCA
Found at i:124835 original size:29 final size:29
Alignment explanation
Indices: 124815--125230 Score: 305
Period size: 30 Copynumber: 14.2 Consensus size: 29
124805 TTTGGGGATT
* *
124815 AAAATGTAATTTTAGAAAGTTTTAGAGGTA
1 AAAATGTAATTTTTGAAAG-TTTAGGGGTA
* * *
124845 AAAATGTCATTTTAGGAAATTTTA-GGGTA
1 AAAATGTAATTTT-TGAAAGTTTAGGGGTA
** * *
124874 AAAACATGATTTTTGAAAG-TTCGAGGGTA
1 AAAATGTAATTTTTGAAAGTTTAG-GGGTA
* * * *
124903 AAAATATTATTTTTGGAAG-TTCGAGGG-A
1 AAAATGTAATTTTTGAAAGTTTAG-GGGTA
* *
124931 AAAAGGTAATTTTTGAGAAGTTTA--GGAA
1 AAAATGTAATTTTTGA-AAGTTTAGGGGTA
124959 CAAAATGTAATTTTTTG-AAGTTTAGGGGT-
1 -AAAATGTAA-TTTTTGAAAGTTTAGGGGTA
* * *
124988 AAAATGTAATTTTTGAGAATTTTAAGGGCA
1 AAAATGTAATTTTTGA-AAGTTTAGGGGTA
* * *
125018 AAAATGTAATTTTTGGAAGTTTAAGGGAA
1 AAAATGTAATTTTTGAAAGTTTAGGGGTA
* *
125047 AAAATATAATTTTTGAGAAGTTTAGGGG-C
1 AAAATGTAATTTTTGA-AAGTTTAGGGGTA
** *
125076 AAAATGTAATTTTTGAAAAGTTTAAAGGTT
1 AAAATGTAATTTTTG-AAAGTTTAGGGGTA
* *
125106 AAAATGTGATTTTGGAAAAGTTTAGGGGTA
1 AAAATGTAATTTTTG-AAAGTTTAGGGGTA
*
125136 AAAATGTAATTTTTGAAAAGGTT-GGGGT-
1 AAAATGTAATTTTTG-AAAGTTTAGGGGTA
* * *
125164 AAAATGTAATTTTTGATAAGTTCAAGGGTC
1 AAAATGTAATTTTTGA-AAGTTTAGGGGTA
* ** *
125194 AAAATGTGATTTTAAAAAAGTTTAGGGGTT
1 AAAATGTAATTTT-TGAAAGTTTAGGGGTA
125224 AAAATGT
1 AAAATGT
125231 GATATTGGAA
Statistics
Matches: 315, Mismatches: 51, Indels: 40
0.78 0.13 0.10
Matches are distributed among these distances:
27 11 0.03
28 53 0.17
29 120 0.38
30 126 0.40
31 5 0.02
ACGTcount: A:0.39, C:0.02, G:0.23, T:0.36
Consensus pattern (29 bp):
AAAATGTAATTTTTGAAAGTTTAGGGGTA
Found at i:124851 original size:30 final size:28
Alignment explanation
Indices: 124815--125230 Score: 302
Period size: 29 Copynumber: 14.2 Consensus size: 28
124805 TTTGGGGATT
*
124815 AAAATGTAATTTTAGAAAGTTTTAGAGGTA
1 AAAATGTAATTTTTGAAAG-TTTAG-GGTA
* * *
124845 AAAATGTCATTTTAGGAAATTTTAGGGTA
1 AAAATGTAATTTT-TGAAAGTTTAGGGTA
** * *
124874 AAAACATGATTTTTGAAAGTTCGAGGGTA
1 AAAATGTAATTTTTGAAAGTT-TAGGGTA
* * * *
124903 AAAATATTATTTTTGGAAGTTCGAGGG-A
1 AAAATGTAATTTTTGAAAGTT-TAGGGTA
* *
124931 AAAAGGTAATTTTTGAGAAGTTTA-GGAA
1 AAAATGTAATTTTTGA-AAGTTTAGGGTA
124959 CAAAATGTAATTTTTTG-AAGTTTAGGGGT-
1 -AAAATGTAA-TTTTTGAAAGTTTA-GGGTA
* *
124988 AAAATGTAATTTTTGAGAATTTTAAGGGCA
1 AAAATGTAATTTTTGA-AAGTTT-AGGGTA
* *
125018 AAAATGTAATTTTTGGAAGTTTAAGGGAA
1 AAAATGTAATTTTTGAAAGTTT-AGGGTA
* **
125047 AAAATATAATTTTTGAGAAGTTTAGGGGC
1 AAAATGTAATTTTTGA-AAGTTTAGGGTA
* *
125076 AAAATGTAATTTTTGAAAAGTTTAAAGGTT
1 AAAATGTAATTTTTG-AAAGTTT-AGGGTA
* *
125106 AAAATGTGATTTTGGAAAAGTTTAGGGGTA
1 AAAATGTAATTTTTG-AAAGTTTA-GGGTA
* *
125136 AAAATGTAATTTTTGAAAAGGTTGGGGT-
1 AAAATGTAATTTTTG-AAAGTTTAGGGTA
* *
125164 AAAATGTAATTTTTGATAAGTTCAAGGGTC
1 AAAATGTAATTTTTGA-AAGTT-TAGGGTA
* ** *
125194 AAAATGTGATTTTAAAAAAGTTTAGGGGTT
1 AAAATGTAATTTT-TGAAAGTTTA-GGGTA
125224 AAAATGT
1 AAAATGT
125231 GATATTGGAA
Statistics
Matches: 317, Mismatches: 48, Indels: 42
0.78 0.12 0.10
Matches are distributed among these distances:
27 9 0.03
28 56 0.18
29 124 0.39
30 123 0.39
31 5 0.02
ACGTcount: A:0.39, C:0.02, G:0.23, T:0.36
Consensus pattern (28 bp):
AAAATGTAATTTTTGAAAGTTTAGGGTA
Found at i:125213 original size:88 final size:88
Alignment explanation
Indices: 124960--125258 Score: 311
Period size: 88 Copynumber: 3.4 Consensus size: 88
124950 GTTTAGGAAC
* * *
124960 AAAATGTAATTTTTTG--AAGTTTAGGGGTAAAATGTAATTTTTGAGAATTTTAAGGG-CAAAAA
1 AAAATGTAA-TTTTTGAAAAGGTTAGGGGTAAAATGTAATTTTTGAAAAGTTTAAGGGTC-AAAA
* *** * *
125022 TGTAATTTTTGGAAGTTTAAGGGAA
64 TGTGATTTTAAAAAGTTTAGGGGTA
* * * * * *
125047 AAAATATAATTTTTGAGAAGTTTAGGGGCAAAATGTAATTTTTGAAAAGTTTAAAGGTTAAAATG
1 AAAATGTAATTTTTGAAAAGGTTAGGGGTAAAATGTAATTTTTGAAAAGTTTAAGGGTCAAAATG
*
125112 TGATTTTGGAAAAGTTTAGGGGTA
66 TGATTTT-AAAAAGTTTAGGGGTA
* *
125136 AAAATGTAATTTTTGAAAAGGTT-GGGGTAAAATGTAATTTTTGATAAGTTCAAGGGTCAAAATG
1 AAAATGTAATTTTTGAAAAGGTTAGGGGTAAAATGTAATTTTTGAAAAGTTTAAGGGTCAAAATG
*
125200 TGATTTTAAAAAAGTTTAGGGGTT
66 TGATTTT-AAAAAGTTTAGGGGTA
* * *
125224 AAAATGTGATATTGGAAAAGCG-TAGGGGTCAAAAT
1 AAAATGTAATTTTTGAAAAG-GTTAGGGGT-AAAAT
125259 ATGTTTTTTA
Statistics
Matches: 179, Mismatches: 26, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
86 6 0.03
87 8 0.04
88 123 0.69
89 37 0.21
90 5 0.03
ACGTcount: A:0.39, C:0.02, G:0.24, T:0.35
Consensus pattern (88 bp):
AAAATGTAATTTTTGAAAAGGTTAGGGGTAAAATGTAATTTTTGAAAAGTTTAAGGGTCAAAATG
TGATTTTAAAAAGTTTAGGGGTA
Found at i:125231 original size:30 final size:30
Alignment explanation
Indices: 124786--125258 Score: 269
Period size: 30 Copynumber: 16.2 Consensus size: 30
124776 AAAGGGGTCG
* * *
124786 AAAATG-AAGTTTCGAAGAGTTT-GGGGATT
1 AAAATGTAATTTTTGAAAAGTTTAGGGG-TT
* * *
124815 AAAATGTAATTTTAG-AAAGTTTTAGAGGTA
1 AAAATGTAATTTTTGAAAAG-TTTAGGGGTT
* * * * *
124845 AAAATGTCATTTTAGGAAATTTTA-GGGTA
1 AAAATGTAATTTTTGAAAAGTTTAGGGGTT
** * * *
124874 AAAACATGATTTTTG-AAAG-TTCGAGGGTA
1 AAAATGTAATTTTTGAAAAGTTTAG-GGGTT
* * * * *
124903 AAAATATTATTTTTG-GAAG-TTCGAGGG-A
1 AAAATGTAATTTTTGAAAAGTTTAG-GGGTT
* * ***
124931 AAAAGGTAATTTTTGAGAAGTTTA-GGAAC
1 AAAATGTAATTTTTGAAAAGTTTAGGGGTT
124960 AAAATGTAATTTTTTG--AAGTTTAGGGG-T
1 AAAATGTAA-TTTTTGAAAAGTTTAGGGGTT
* * * **
124988 AAAATGTAATTTTTGAGAATTTTAAGGGCA
1 AAAATGTAATTTTTGAAAAGTTTAGGGGTT
* * **
125018 AAAATGTAATTTTTG-GAAGTTTAAGGGAA
1 AAAATGTAATTTTTGAAAAGTTTAGGGGTT
* * *
125047 AAAATATAATTTTTGAGAAGTTTAGGGG-C
1 AAAATGTAATTTTTGAAAAGTTTAGGGGTT
**
125076 AAAATGTAATTTTTGAAAAGTTTAAAGGTT
1 AAAATGTAATTTTTGAAAAGTTTAGGGGTT
* * *
125106 AAAATGTGATTTTGGAAAAGTTTAGGGGTA
1 AAAATGTAATTTTTGAAAAGTTTAGGGGTT
*
125136 AAAATGTAATTTTTGAAAAGGTT-GGGG-T
1 AAAATGTAATTTTTGAAAAGTTTAGGGGTT
* * * *
125164 AAAATGTAATTTTTGATAAGTTCAAGGGTC
1 AAAATGTAATTTTTGAAAAGTTTAGGGGTT
* **
125194 AAAATGTGATTTTAAAAAAGTTTAGGGGTT
1 AAAATGTAATTTTTGAAAAGTTTAGGGGTT
* * * ** *
125224 AAAATGTGATATTGGAAAAGCGTAGGGGTC
1 AAAATGTAATTTTTGAAAAGTTTAGGGGTT
125254 AAAAT
1 AAAAT
125259 ATGTTTTTTA
Statistics
Matches: 360, Mismatches: 66, Indels: 35
0.78 0.14 0.08
Matches are distributed among these distances:
27 8 0.02
28 54 0.15
29 133 0.37
30 159 0.44
31 6 0.02
ACGTcount: A:0.39, C:0.03, G:0.24, T:0.35
Consensus pattern (30 bp):
AAAATGTAATTTTTGAAAAGTTTAGGGGTT
Found at i:125267 original size:118 final size:116
Alignment explanation
Indices: 125047--125267 Score: 291
Period size: 118 Copynumber: 1.9 Consensus size: 116
125037 TTTAAGGGAA
* **
125047 AAAATATAATTTTTGAGAAGTTTAGGGGCAAAATGTAATTTTTGAAAAGTTTAAAGGTTAAAATG
1 AAAATATAATTTTTGAGAAGTTAAGGGGCAAAATGTAATTTTAAAAAAGTTTAAAGGTTAAAATG
* **
125112 TGATTTTGGAAAAGTTTAGGGGTAAAAATGTAATTTTTGAAAAGGTTGGGGT
66 TGATATTGGAAAAGCGTAGGGGTAAAAATGT-ATTTTTGAAAAGGTTGGGGT
* * * * **
125164 AAAATGTAATTTTTGATAAGTTCAAGGGTCAAAATGTGATTTTAAAAAAGTTTAGGGGTTAAAAT
1 AAAATATAATTTTTGAGAAGTT-AAGGGGCAAAATGTAATTTTAAAAAAGTTTAAAGGTTAAAAT
125229 GTGATATTGGAAAAGCGTAGGGGTCAAAATATGT-TTTTT
65 GTGATATTGGAAAAGCGTAGGGGT-AAAA-ATGTATTTTT
125268 AGACAGTTCA
Statistics
Matches: 89, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
117 20 0.22
118 61 0.69
119 4 0.04
120 4 0.04
ACGTcount: A:0.38, C:0.02, G:0.24, T:0.36
Consensus pattern (116 bp):
AAAATATAATTTTTGAGAAGTTAAGGGGCAAAATGTAATTTTAAAAAAGTTTAAAGGTTAAAATG
TGATATTGGAAAAGCGTAGGGGTAAAAATGTATTTTTGAAAAGGTTGGGGT
Found at i:126897 original size:17 final size:16
Alignment explanation
Indices: 126874--126933 Score: 59
Period size: 17 Copynumber: 3.7 Consensus size: 16
126864 AAATTTAATT
126874 TAAAATAAATTCAAAC
1 TAAAATAAATTCAAAC
* * *
126890 TCAAAATAAGTTTAAATT
1 T-AAAATAAATTCAAA-C
126908 TAAAA-AAATTCAAAC
1 TAAAATAAATTCAAAC
*
126923 TTAAATAAATT
1 TAAAATAAATT
126934 AAAATATAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
15 4 0.12
16 13 0.38
17 16 0.47
18 1 0.03
ACGTcount: A:0.58, C:0.08, G:0.02, T:0.32
Consensus pattern (16 bp):
TAAAATAAATTCAAAC
Found at i:126932 original size:16 final size:16
Alignment explanation
Indices: 126876--126933 Score: 62
Period size: 16 Copynumber: 3.6 Consensus size: 16
126866 ATTTAATTTA
*
126876 AAATAAATTCAAACTCA
1 AAATAAATTCAAACT-T
* * *
126893 AAATAAGTTTAAATTT
1 AAATAAATTCAAACTT
*
126909 AAAAAAATTCAAACTT
1 AAATAAATTCAAACTT
126925 AAATAAATT
1 AAATAAATT
126934 AAAATATAAA
Statistics
Matches: 32, Mismatches: 9, Indels: 1
0.76 0.21 0.02
Matches are distributed among these distances:
16 20 0.62
17 12 0.38
ACGTcount: A:0.59, C:0.09, G:0.02, T:0.31
Consensus pattern (16 bp):
AAATAAATTCAAACTT
Found at i:127491 original size:78 final size:77
Alignment explanation
Indices: 127386--127945 Score: 496
Period size: 78 Copynumber: 7.2 Consensus size: 77
127376 TGCCTCATGA
* * * ** * * **
127386 TCGGGGTAAGAAATTAGCTGATAATGATCTGCACCAGGCTCAAGGTAAGAGGTCGAATGGCTGTA
1 TCGGGGTAAGAGATTGGCTGATGATGATCTGC-CCAGGCTCGGGGTAAAAGATCGAATGGCTACA
127451 ATTTGCCCTAGGC
65 ATTTGCCCTAGGC
* * * *
127464 TCGGGGTAAGAGATTGGCTGATGATGATCTGTCCAAGGCTCGGGGTAAAAGATTGAACGACTACA
1 TCGGGGTAAGAGATTGGCTGATGATGATCTG-CCCAGGCTCGGGGTAAAAGATCGAATGGCTACA
* * *
127529 ATCTGCCCCAGGG
65 ATTTGCCCTAGGC
* * * * * *
127542 TCGGGGTAAGAGATTTGCTGATGGTGATCTGGCCTAGGCTCGGGGTAAAAGATTGAATAGTTACA
1 TCGGGGTAAGAGATTGGCTGATGATGATCT-GCCCAGGCTCGGGGTAAAAGATCGAATGGCTACA
* *
127607 ATCTGCCCCAGGC
65 ATTTGCCCTAGGC
* * * * * * **
127620 TCGGGGTAAGAGATTGGCAGATGCTGATCTACCCTAGGTTCGGGGTAAAGGGTCGAATGGCTTTA
1 TCGGGGTAAGAGATTGGCTGATGATGATCTGCCC-AGGCTCGGGGTAAAAGATCGAATGGCTACA
*
127685 ATCTGCCCTAGGC
65 ATTTGCCCTAGGC
* * * * ** *
127698 TCGGGGTAAGAGATTGGCTGACGACGATCTACCCCAAGCTTAGGGTAAAAGATCGAATGACTACA
1 TCGGGGTAAGAGATTGGCTGATGATGATCT-GCCCAGGCTCGGGGTAAAAGATCGAATGGCTACA
* *
127763 ATTT-TCCTAAAGC
65 ATTTGCCCT-AGGC
* * * * * * *
127776 TCGGAGTAAGAGATTGGCTGATGGTGATCTACCCTAGGCTCGGGTTAAAAGATCAAATGACTGCA
1 TCGGGGTAAGAGATTGGCTGATGATGATCTGCCC-AGGCTCGGGGTAAAAGATCGAATGGCTACA
127841 ATTTGCCAC-AGGC
65 ATTTGCC-CTAGGC
* * * * * **
127854 TAGGGTTAAGAGATTGGCTGATGATGATCTGCCCTAGGTTCGGGGTAAAGGATCGAACGGCTGTA
1 TCGGGGTAAGAGATTGGCTGATGATGATCTGCCC-AGGCTCGGGGTAAAAGATCGAATGGCTACA
127919 ATTTG-CCTCAGGC
65 ATTTGCCCT-AGGC
*
127932 TCGGGGTAAAAGAT
1 TCGGGGTAAGAGAT
127946 CGAACGGCTG
Statistics
Matches: 389, Mismatches: 83, Indels: 20
0.79 0.17 0.04
Matches are distributed among these distances:
76 1 0.00
77 9 0.02
78 372 0.96
79 6 0.02
80 1 0.00
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (77 bp):
TCGGGGTAAGAGATTGGCTGATGATGATCTGCCCAGGCTCGGGGTAAAAGATCGAATGGCTACAA
TTTGCCCTAGGC
Found at i:127503 original size:39 final size:39
Alignment explanation
Indices: 127386--128335 Score: 300
Period size: 39 Copynumber: 24.4 Consensus size: 39
127376 TGCCTCATGA
* * * *
127386 TCGGGGTAAGAAATTAGCTGATAATGATCTGCACCAGGC
1 TCGGGGTAAGAGATTGGCTGATGATGATCTGCCCCAGGC
** * * ** * * * *
127425 TCAAGGTAAGAGGTCGAATGGCTG-TAATTTGCCCTAGGC
1 TCGGGGTAAGAGATTGGCT-GATGATGATCTGCCCCAGGC
* *
127464 TCGGGGTAAGAGATTGGCTGATGATGATCTGTCCAAGGC
1 TCGGGGTAAGAGATTGGCTGATGATGATCTGCCCCAGGC
* * ** *
127503 TCGGGGTAAAAGATTGAAC-GACT-ACAATCTGCCCCAGGG
1 TCGGGGTAAGAGATTG-GCTGA-TGATGATCTGCCCCAGGC
* * * *
127542 TCGGGGTAAGAGATTTGCTGATGGTGATCTGGCCTAGGC
1 TCGGGGTAAGAGATTGGCTGATGATGATCTGCCCCAGGC
* ** * **
127581 TCGGGGTAAAAGATTGAAT-AGTTACAATCTGCCCCAGGC
1 TCGGGGTAAGAGATTGGCTGA-TGATGATCTGCCCCAGGC
* * * * *
127620 TCGGGGTAAGAGATTGGCAGATGCTGATCTACCCTAGGT
1 TCGGGGTAAGAGATTGGCTGATGATGATCTGCCCCAGGC
* * * *
127659 TCGGGGTAAAGGGTCGAATGGCT--T--TAATCTGCCCTAGGC
1 TCGGGGT-AA--G-AGATTGGCTGATGATGATCTGCCCCAGGC
* * * *
127698 TCGGGGTAAGAGATTGGCTGACGACGATCTACCCCAAGC
1 TCGGGGTAAGAGATTGGCTGATGATGATCTGCCCCAGGC
** * * ** ** * * ** *
127737 TTAGGGTAAAAGATCGAATGACT-ACAATTTTCCTAAAGC
1 TCGGGGTAAGAGATTGGCTGA-TGATGATCTGCCCCAGGC
* * * *
127776 TCGGAGTAAGAGATTGGCTGATGGTGATCTACCCTAGGC
1 TCGGGGTAAGAGATTGGCTGATGATGATCTGCCCCAGGC
* * ** * *
127815 TCGGGTTAAAAGA-T--CAAATGACTGCAATTTGCCACAGGC
1 TCGGGGTAAGAGATTGGCTGATGA-TG--ATCTGCCCCAGGC
* * * *
127854 TAGGGTTAAGAGATTGGCTGATGATGATCTGCCCTAGGT
1 TCGGGGTAAGAGATTGGCTGATGATGATCTGCCCCAGGC
* * * * * * *
127893 TCGGGGTAA-AGGATCGAACGGCTG-TAATTTGCCTCAGGC
1 TCGGGGTAAGA-GATTG-GCTGATGATGATCTGCCCCAGGC
* * * * * *
127932 TCGGGGTAAAAGATCGAACGGCTGCA--ATCTACCCCAGGC
1 TCGGGGTAAGAGATTG-GCTGATG-ATGATCTGCCCCAGGC
* * * * *
127971 TCGAGGTAAGAGATTGGCTAATGATGATTTGACCCAAGC
1 TCGGGGTAAGAGATTGGCTGATGATGATCTGCCCCAGGC
* * * * * *
128010 TTGGGGTAAAAGATTGAACGGTTGCA--ATCTGCCCTAGGC
1 TCGGGGTAAGAGATTG-GCTGATG-ATGATCTGCCCCAGGC
* * * *
128049 TCGGGGTAAGAGATTGGTTGATGGTGATTTGCCCTAGGC
1 TCGGGGTAAGAGATTGGCTGATGATGATCTGCCCCAGGC
* * ** * * *
128088 TCGGGGTAAAAGA-TCG-AAATGTTGCAATCTGCCTCATGC
1 TCGGGGTAAGAGATTGGCTGATGATG--ATCTGCCCCAGGC
* * * *
128127 TCGGGGTAAGAGATTGACTGATGGTGATCTGCCCCAAGT
1 TCGGGGTAAGAGATTGGCTGATGATGATCTGCCCCAGGC
* *
128166 TCGGGGTAAAAGATCAAATGGCTG--CA--ATCTAG-CCCAGGC
1 TCGGGGTAAGAGAT----TGGCTGATGATGATCT-GCCCCAGGC
* * *
128205 TCGGGGTAAGAGATTGGCTGATAATGATCTACCCTAGGC
1 TCGGGGTAAGAGATTGGCTGATGATGATCTGCCCCAGGC
* * * * * *
128244 TCGAGGTAAAAGATCGAAC-GA-CA-GCAATCTGCTCCAGGC
1 TCGGGGTAAGAGATTG-GCTGATGATG--ATCTGCCCCAGGC
* * * ** *
128283 TCGAGGTAAGAGATTGGTTGATGGTGATCTGCCTTAGGT
1 TCGGGGTAAGAGATTGGCTGATGATGATCTGCCCCAGGC
*
128322 TTGGGGTAAGAGAT
1 TCGGGGTAAGAGAT
128336 CGAATCTTCA
Statistics
Matches: 643, Mismatches: 213, Indels: 110
0.67 0.22 0.11
Matches are distributed among these distances:
35 13 0.02
36 5 0.01
37 10 0.02
38 20 0.03
39 549 0.85
40 19 0.03
41 10 0.02
42 6 0.01
43 11 0.02
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.24
Consensus pattern (39 bp):
TCGGGGTAAGAGATTGGCTGATGATGATCTGCCCCAGGC
Found at i:127787 original size:234 final size:234
Alignment explanation
Indices: 127436--127945 Score: 657
Period size: 234 Copynumber: 2.2 Consensus size: 234
127426 CAAGGTAAGA
* * **
127436 GGTCGAATGGCTGTAATTTGCCCTAGGCTCGGGGTAAGAGATTGGCTGATGATGATCTGTCCAAG
1 GGTCGAATGGCTGTAATTTGCCCTAGGCTCGGGGTAAGAGATTGGCTGACGACGATCTCCCCAAG
* * * * * * *
127501 GCTCGGGGTAAAAGATTGAACGACTACAATCTGCCCCAGGGTCGGGGTAAGAGATTTGCTGATGG
66 GCTCAGGGTAAAAGATCGAACGACTACAATCTGCCCAAAGCTCGGAGTAAGAGATTGGCTGATGG
** ** * * *
127566 TGATCTGGCCTAGGCTCGGGGTAAAAGATTGAAT-AGTTACAATCTGCCCCAGGCTCGGGGTAAG
131 TGATCTACCCTAGGCTCGGGGTAAAAGATCAAATGA-CTACAATCTGCCACAGGCTAGGGGTAAG
*
127630 AGATTGGCAGATGCTGATCTACCCTAGGTTCGGGGTAAAG
195 AGATTGGCAGATGATGATCTACCCTAGGTTCGGGGTAAAG
* *
127670 GGTCGAATGGCTTTAATCTGCCCTAGGCTCGGGGTAAGAGATTGGCTGACGACGATCTACCCCAA
1 GGTCGAATGGCTGTAATTTGCCCTAGGCTCGGGGTAAGAGATTGGCTGACGACGATCT-CCCCAA
* * * * *
127735 -GCTTAGGGTAAAAGATCGAATGACTACAATTTTCCTAAAGCTCGGAGTAAGAGATTGGCTGATG
65 GGCTCAGGGTAAAAGATCGAACGACTACAATCTGCCCAAAGCTCGGAGTAAGAGATTGGCTGATG
* * * *
127799 GTGATCTACCCTAGGCTCGGGTTAAAAGATCAAATGACTGCAATTTGCCACAGGCTAGGGTTAAG
130 GTGATCTACCCTAGGCTCGGGGTAAAAGATCAAATGACTACAATCTGCCACAGGCTAGGGGTAAG
* *
127864 AGATTGGCTGATGATGATCTGCCCTAGGTTCGGGGTAAAG
195 AGATTGGCAGATGATGATCTACCCTAGGTTCGGGGTAAAG
* * *
127904 GATCGAACGGCTGTAATTTG-CCTCAGGCTCGGGGTAAAAGAT
1 GGTCGAATGGCTGTAATTTGCCCT-AGGCTCGGGGTAAGAGAT
127946 CGAACGGCTG
Statistics
Matches: 236, Mismatches: 37, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
233 3 0.01
234 228 0.97
235 5 0.02
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.25
Consensus pattern (234 bp):
GGTCGAATGGCTGTAATTTGCCCTAGGCTCGGGGTAAGAGATTGGCTGACGACGATCTCCCCAAG
GCTCAGGGTAAAAGATCGAACGACTACAATCTGCCCAAAGCTCGGAGTAAGAGATTGGCTGATGG
TGATCTACCCTAGGCTCGGGGTAAAAGATCAAATGACTACAATCTGCCACAGGCTAGGGGTAAGA
GATTGGCAGATGATGATCTACCCTAGGTTCGGGGTAAAG
Found at i:128001 original size:78 final size:77
Alignment explanation
Indices: 127922--128339 Score: 451
Period size: 78 Copynumber: 5.4 Consensus size: 77
127912 GGCTGTAATT
* *
127922 TGCCTCAGGCTCGGGGTAAAAGATCGAACGGCTGCAATCTACCCCAGGCTCGAGGTAAGAGATTG
1 TGCC-CAGGCTCGGGGTAAAAGATCGAACGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTG
* * *
127987 GCTAATGATGATT
65 GCTGATGGTGATC
* * * * *
128000 TGACCCAAGCTTGGGGTAAAAGATTGAACGGTTGCAATCTGCCCTAGGCTCGGGGTAAGAGATTG
1 TG-CCCAGGCTCGGGGTAAAAGATCGAACGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTG
* *
128065 GTTGATGGTGATT
65 GCTGATGGTGATC
** * * *
128078 TGCCCTAGGCTCGGGGTAAAAGATCGAAATGTTGCAATCTGCCTCATGCTCGGGGTAAGAGATTG
1 TGCCC-AGGCTCGGGGTAAAAGATCGAACGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTG
*
128143 ACTGATGGTGATC
65 GCTGATGGTGATC
* * * *
128156 TGCCCCAAGTTCGGGGTAAAAGATCAAATGGCTGCAATCTAG-CCCAGGCTCGGGGTAAGAGATT
1 TG-CCCAGGCTCGGGGTAAAAGATCGAACGGCTGCAATCT-GCCCCAGGCTCGGGGTAAGAGATT
**
128220 GGCTGATAATGATC
64 GGCTGATGGTGATC
* * * * * *
128234 TACCCTAGGCTCGAGGTAAAAGATCGAACGACAGCAATCTGCTCCAGGCTCGAGGTAAGAGATTG
1 TGCCC-AGGCTCGGGGTAAAAGATCGAACGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTG
*
128299 GTTGATGGTGATC
65 GCTGATGGTGATC
* * * *
128312 TGCCTTAGGTTTGGGGTAAGAGATCGAA
1 TGCC-CAGGCTCGGGGTAAAAGATCGAA
128340 TCTTCAATTT
Statistics
Matches: 282, Mismatches: 51, Indels: 14
0.81 0.15 0.04
Matches are distributed among these distances:
77 7 0.02
78 269 0.95
79 6 0.02
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.24
Consensus pattern (77 bp):
TGCCCAGGCTCGGGGTAAAAGATCGAACGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGG
CTGATGGTGATC
Found at i:128024 original size:156 final size:156
Alignment explanation
Indices: 127880--128298 Score: 416
Period size: 156 Copynumber: 2.7 Consensus size: 156
127870 GCTGATGATG
* *
127880 ATCTGCCCTAGGTTCGGGGTAA-AGGATCGAACGGCT-GTAATTTG-CCTCAGGCTCGGGGTAAA
1 ATCTGCCCTAGGCTCGGGGTAAGA-GATCG-ACGGATGGTAATTTGCCCT-AGGCTCGGGGTAAA
* * *
127942 AGATCGAACGGCTGCAATCTACCCCAGGCTCGAGGTAAGAGATTGGCTAATGATGATTTGACCCA
63 AGATCGAAAGGCTGCAATCTACCCCAGGCTCGAGGTAAGAGATTGACTAATGATGATCTGACCCA
*
128007 AGCTT-GGGGTAAAAGATTGAACGGTTGCA
128 AG-TTCGGGGTAAAAGATTGAACGGATGCA
* *** *
128036 ATCTGCCCTAGGCTCGGGGTAAGAGATTGGTTGATGGTGATTTGCCCTAGGCTCGGGGTAAAAGA
1 ATCTGCCCTAGGCTCGGGGTAAGAGATCGACGGATGGTAATTTGCCCTAGGCTCGGGGTAAAAGA
* * * * * * * * *
128101 TCGAAATGTTGCAATCTGCCTCATGCTCGGGGTAAGAGATTGACTGATGGTGATCTGCCCCAAGT
66 TCGAAAGGCTGCAATCTACCCCAGGCTCGAGGTAAGAGATTGACTAATGATGATCTGACCCAAGT
** * *
128166 TCGGGGTAAAAGATCAAATGGCTGCA
131 TCGGGGTAAAAGATTGAACGGATGCA
* * * ** * * * *
128192 ATCTAGCCC-AGGCTCGGGGTAAGAGATTGGCTGATAATGATCTACCCTAGGCTCGAGGTAAAAG
1 ATCT-GCCCTAGGCTCGGGGTAAGAGATCGACGGATGGTAATTTGCCCTAGGCTCGGGGTAAAAG
* * * * *
128256 ATCGAACGACAGCAATCTGCTCCAGGCTCGAGGTAAGAGATTG
65 ATCGAAAGGCTGCAATCTACCCCAGGCTCGAGGTAAGAGATTG
128299 GTTGATGGTG
Statistics
Matches: 220, Mismatches: 38, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
155 4 0.02
156 208 0.95
157 8 0.04
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.23
Consensus pattern (156 bp):
ATCTGCCCTAGGCTCGGGGTAAGAGATCGACGGATGGTAATTTGCCCTAGGCTCGGGGTAAAAGA
TCGAAAGGCTGCAATCTACCCCAGGCTCGAGGTAAGAGATTGACTAATGATGATCTGACCCAAGT
TCGGGGTAAAAGATTGAACGGATGCA
Found at i:139833 original size:30 final size:29
Alignment explanation
Indices: 139799--140216 Score: 250
Period size: 30 Copynumber: 14.2 Consensus size: 29
139789 TTAAAATGCA
* *
139799 ATTTTAGAAAGTTTTAGGGGTAAAAATGTT
1 ATTTTGGAAAG-TTTAGGGGTAAAAATGTG
*
139829 ATTTTAGGAAAATTT-GGGGTAAAAATGTG
1 ATTTT-GGAAAGTTTAGGGGTAAAAATGTG
*
139858 ATTTTTGG-AAG-TTCGAGGGTAAAAATGTG
1 A-TTTTGGAAAGTTTAG-GGGTAAAAATGTG
* * *
139887 ATTTTTGGAAA-TTT-GTAGGCAAAAATGTA
1 A-TTTTGGAAAGTTTAG-GGGTAAAAATGTG
* * *
139916 ATTTTTGG-AAGTTCAGGGG--AAAATTTA
1 A-TTTTGGAAAGTTTAGGGGTAAAAATGTG
* * *
139943 ATTTTTGAGAAGTTTAGAGGTAAAAATGTA
1 ATTTTGGA-AAGTTTAGGGGTAAAAATGTG
** * *
139973 ATTTTTAAGAAGTTT-GACGGTCAAAATGTG
1 ATTTTGGA-AAGTTTAG-GGGTAAAAATGTG
** * *
140003 ATTTTGGAAAAGTTT-GAAAGCAAAAATAT-
1 ATTTTGG-AAAGTTTAG-GGGTAAAAATGTG
* * *
140032 ATTTTTTGAAAGTTTAGGGGTAAAAACGTAA
1 A-TTTTGGAAAGTTTAGGGGTAAAAATGT-G
*
140063 ATTTT-GAGAAGTTTAGGGGTCAAAATGTG
1 ATTTTGGA-AAGTTTAGGGGTAAAAATGTG
* *
140092 ATTTTGGAAAAGTTCTA-GGGTAAAAATATA
1 ATTTTGG-AAAGTT-TAGGGGTAAAAATGTG
* * *
140122 ATTTTTGAGAAGTTTAAGGGTTAAAATGTG
1 ATTTTGGA-AAGTTTAGGGGTAAAAATGTG
* *
140152 ATTTTGGAAAAGTTTAAGGGTTAAAATGTG
1 ATTTTGG-AAAGTTTAGGGGTAAAAATGTG
* * *
140182 ATTTTGGAAAAGTATAGGGGTCAAAATATG
1 ATTTTGG-AAAGTTTAGGGGTAAAAATGTG
140212 ATTTT
1 ATTTT
140217 TTGATAGTTC
Statistics
Matches: 316, Mismatches: 47, Indels: 50
0.77 0.11 0.12
Matches are distributed among these distances:
26 5 0.02
27 10 0.03
28 14 0.04
29 86 0.27
30 191 0.60
31 10 0.03
ACGTcount: A:0.37, C:0.02, G:0.24, T:0.36
Consensus pattern (29 bp):
ATTTTGGAAAGTTTAGGGGTAAAAATGTG
Found at i:140057 original size:89 final size:89
Alignment explanation
Indices: 139935--140194 Score: 319
Period size: 89 Copynumber: 2.9 Consensus size: 89
139925 AGTTCAGGGG
* * *
139935 AAAATTTAATTTTTGAGAAGTTTAGAGGTAAAAATGTAATTTTTAAGAAGTTTGACGGTCAAAAT
1 AAAATATAATTTTTGAGAAGTTTAGGGGTAAAAATGTAATTTTTAAGAAGTTT-AGGGTCAAAAT
140000 GTGATTTTGGAAAAGTT-TGAAAGCA
65 GTGATTTTGGAAAAGTTCT-AAAGCA
* * * *
140025 AAAATATATTTTTTGA-AAGTTTAGGGGTAAAAACGTAAATTTTGAGAAGTTTAGGGGTCAAAAT
1 AAAATATAATTTTTGAGAAGTTTAGGGGTAAAAATGTAATTTTTAAGAAGTTTA-GGGTCAAAAT
** *
140089 GTGATTTTGGAAAAGTTCTAGGGTA
65 GTGATTTTGGAAAAGTTCTAAAGCA
* * * * *
140114 AAAATATAATTTTTGAGAAGTTTAAGGGTTAAAATGTGATTTTGGAA-AAGTTTAAGGGTTAAAA
1 AAAATATAATTTTTGAGAAGTTTAGGGGTAAAAATGTAATTTT-TAAGAAGTTT-AGGGTCAAAA
140178 TGTGATTTTGGAAAAGT
64 TGTGATTTTGGAAAAGT
140195 ATAGGGGTCA
Statistics
Matches: 146, Mismatches: 19, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
88 1 0.01
89 76 0.52
90 67 0.46
91 2 0.01
ACGTcount: A:0.39, C:0.02, G:0.23, T:0.36
Consensus pattern (89 bp):
AAAATATAATTTTTGAGAAGTTTAGGGGTAAAAATGTAATTTTTAAGAAGTTTAGGGTCAAAATG
TGATTTTGGAAAAGTTCTAAAGCA
Found at i:141096 original size:14 final size:14
Alignment explanation
Indices: 141077--141103 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
141067 TATTAATAAT
141077 ATTATTTATTTAAA
1 ATTATTTATTTAAA
141091 ATTATTTATTTAA
1 ATTATTTATTTAA
141104 TACGTTTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
ATTATTTATTTAAA
Found at i:141770 original size:17 final size:17
Alignment explanation
Indices: 141748--141797 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
141738 AATTTAATTT
141748 AAAATAAATTCAAACTC
1 AAAATAAATTCAAACTC
* * * *
141765 AAAATAAGTTTAAATTT
1 AAAATAAATTCAAACTC
141782 AAAATAAATTCAAACT
1 AAAATAAATTCAAACT
141798 TATAAAATTT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.58, C:0.10, G:0.02, T:0.30
Consensus pattern (17 bp):
AAAATAAATTCAAACTC
Found at i:143218 original size:13 final size:13
Alignment explanation
Indices: 143200--143229 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
143190 AAAGAAATAG
*
143200 TTTTTTCCTTCGT
1 TTTTTTCCTTCAT
143213 TTTTTTCCTTCAT
1 TTTTTTCCTTCAT
143226 TTTT
1 TTTT
143230 GTCTTGTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.03, C:0.20, G:0.03, T:0.73
Consensus pattern (13 bp):
TTTTTTCCTTCAT
Found at i:144112 original size:45 final size:45
Alignment explanation
Indices: 144010--144315 Score: 302
Period size: 45 Copynumber: 7.1 Consensus size: 45
144000 GGTTTTGTGA
* *
144010 GATGGTAGCTTCAATCT-GTCCCTCTTGATTTAAGGGTAAAAGATTG
1 GATGGTGGCTTCAATCTAG-CCCTCTTGA-TTAGGGGTAAAAGATTG
* * *
144056 GACGGTTGCTTCAATCTAGCCCTCTTCATTAGGGGTAAAAGATTG
1 GATGGTGGCTTCAATCTAGCCCTCTTGATTAGGGGTAAAAGATTG
*
144101 GATGGTGGCTTCAATCTACCCCTCTTGATTAGGGGTAAAAGATTG
1 GATGGTGGCTTCAATCTAGCCCTCTTGATTAGGGGTAAAAGATTG
* **
144146 GATGGTGGCTTCAATCT-TCCTCTCTCAATTAGGGGTAAAAGATTG
1 GATGGTGGCTTCAATCTAGCC-CTCTTGATTAGGGGTAAAAGATTG
* * *
144191 AATGGT--CTTCAATCTACCCCTCTTGACTAGGGGTAAAAGATTG
1 GATGGTGGCTTCAATCTAGCCCTCTTGATTAGGGGTAAAAGATTG
* * * *
144234 GA---T-GCTTCAATCTA--CCTCATGGTCA-GGGTAAGAGATTG
1 GATGGTGGCTTCAATCTAGCCCTCTTGATTAGGGGTAAAAGATTG
* * *
144272 G-T-GTGTCTTCAATCT-GCCATC-TAATTA-GGGTAAAAGATTG
1 GATGGTGGCTTCAATCTAGCCCTCTTGATTAGGGGTAAAAGATTG
144312 GATG
1 GATG
144316 CTTCAATCTG
Statistics
Matches: 221, Mismatches: 28, Indels: 26
0.80 0.10 0.09
Matches are distributed among these distances:
38 13 0.06
39 8 0.04
40 26 0.12
41 14 0.06
43 31 0.14
44 4 0.02
45 101 0.46
46 23 0.10
47 1 0.00
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.32
Consensus pattern (45 bp):
GATGGTGGCTTCAATCTAGCCCTCTTGATTAGGGGTAAAAGATTG
Found at i:144271 original size:38 final size:38
Alignment explanation
Indices: 144221--144353 Score: 144
Period size: 38 Copynumber: 3.4 Consensus size: 38
144211 TCTTGACTAG
*
144221 GGGTAAAAGATTGGATGCTTCAATCTACCTCATGGTCA
1 GGGTAAAAGATTGGATGCTTCAATCTGCCTCATGGTCA
* * ** *
144259 GGGTAAGAGATTGGTGTGTCTTCAATCTGCCATC-TAATTA
1 GGGTAAAAGATTGG-ATG-CTTCAATCTGCC-TCATGGTCA
*
144299 GGGTAAAAGATTGGATGCTTCAATCTGCCCCATGGTC-
1 GGGTAAAAGATTGGATGCTTCAATCTGCCTCATGGTCA
*
144336 GGAGTAAGAGATTGGATG
1 GG-GTAAAAGATTGGATG
144354 ATAGCTTCTC
Statistics
Matches: 77, Mismatches: 13, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
37 3 0.04
38 41 0.53
39 4 0.05
40 27 0.35
41 2 0.03
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (38 bp):
GGGTAAAAGATTGGATGCTTCAATCTGCCTCATGGTCA
Found at i:144576 original size:24 final size:24
Alignment explanation
Indices: 144544--144595 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
144534 AAATGAGTCA
*
144544 AATGCTCCTTACTAGATAGGTATG
1 AATGCTCCTAACTAGATAGGTATG
*
144568 AATGCTCCTAACTTGATAGGTATG
1 AATGCTCCTAACTAGATAGGTATG
144592 AATG
1 AATG
144596 ATGAATGCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.33
Consensus pattern (24 bp):
AATGCTCCTAACTAGATAGGTATG
Found at i:145311 original size:13 final size:12
Alignment explanation
Indices: 145290--145349 Score: 61
Period size: 12 Copynumber: 4.8 Consensus size: 12
145280 CCTTGACCTC
145290 TTCTTTTCTTT-T
1 TTCTTTT-TTTCT
145302 TTCTTTTTCTT-T
1 TTCTTTTT-TTCT
*
145314 TATATTTTTTTCT
1 T-TCTTTTTTTCT
145327 TTCTTTATTTTCT
1 TTCTTT-TTTTCT
145340 TTCTTTTTTT
1 TTCTTTTTTT
145350 GGGTAAAATT
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
11 1 0.02
12 21 0.50
13 20 0.48
ACGTcount: A:0.05, C:0.13, G:0.00, T:0.82
Consensus pattern (12 bp):
TTCTTTTTTTCT
Found at i:146266 original size:17 final size:18
Alignment explanation
Indices: 146244--146285 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
146234 TCATCTTGAC
146244 TTTTTTCTTC-TTTTCTT
1 TTTTTTCTTCTTTTTCTT
146261 TTTTTT-TTCTTTTTCTT
1 TTTTTTCTTCTTTTTCTT
146278 TTTGTTTC
1 TTT-TTTC
146286 AAGATGCCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 3 0.14
17 16 0.73
18 3 0.14
ACGTcount: A:0.00, C:0.14, G:0.02, T:0.83
Consensus pattern (18 bp):
TTTTTTCTTCTTTTTCTT
Found at i:151857 original size:24 final size:24
Alignment explanation
Indices: 151825--151873 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
151815 AAACAAAGGG
151825 ATTTGGAGGGTCTTTCGGGCTTCA
1 ATTTGGAGGGTCTTTCGGGCTTCA
*
151849 ATTTGGAGGGTCTTTCGGGTTTCA
1 ATTTGGAGGGTCTTTCGGGCTTCA
151873 A
1 A
151874 AGACGCTACC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.14, C:0.14, G:0.33, T:0.39
Consensus pattern (24 bp):
ATTTGGAGGGTCTTTCGGGCTTCA
Found at i:154399 original size:24 final size:24
Alignment explanation
Indices: 154367--154415 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
154357 CATTGTCAAA
*
154367 ACATGGGAAAGACCTGAGCTGTAT
1 ACATGGGAAAGACCTGAGCTATAT
154391 ACATGGGAAAGACCTGAGCTATAT
1 ACATGGGAAAGACCTGAGCTATAT
154415 A
1 A
154416 AAAGGGTGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.16, G:0.27, T:0.20
Consensus pattern (24 bp):
ACATGGGAAAGACCTGAGCTATAT
Found at i:158577 original size:27 final size:27
Alignment explanation
Indices: 158539--158592 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
158529 CATTTAACTA
158539 TCGAATTAATTGCATAAATACATATGT
1 TCGAATTAATTGCATAAATACATATGT
158566 TCGAATTAATTGCATAAATACATATGT
1 TCGAATTAATTGCATAAATACATATGT
158593 AATTCAACAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.37
Consensus pattern (27 bp):
TCGAATTAATTGCATAAATACATATGT
Found at i:159462 original size:21 final size:21
Alignment explanation
Indices: 159416--159472 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 21
159406 ATAGTGTAGA
*
159416 CTTCTACCGATACCTATGACAG
1 CTTCTACCGATA-CAATGACAG
159438 -TTCTACCGATACAAGTGA-AG
1 CTTCTACCGATACAA-TGACAG
*
159458 CTTCTACCGAAACAA
1 CTTCTACCGATACAA
159473 ATCATGCTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 4 0.13
21 27 0.87
ACGTcount: A:0.33, C:0.28, G:0.14, T:0.25
Consensus pattern (21 bp):
CTTCTACCGATACAATGACAG
Found at i:159481 original size:21 final size:21
Alignment explanation
Indices: 159438--159482 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
159428 CCTATGACAG
* * *
159438 TTCTACCGATACAAGTGAAGC
1 TTCTACCGAAACAAATCAAGC
*
159459 TTCTACCGAAACAAATCATGC
1 TTCTACCGAAACAAATCAAGC
159480 TTC
1 TTC
159483 CGCGAGTACT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.27, G:0.13, T:0.27
Consensus pattern (21 bp):
TTCTACCGAAACAAATCAAGC
Found at i:160540 original size:102 final size:102
Alignment explanation
Indices: 160385--160636 Score: 326
Period size: 102 Copynumber: 2.5 Consensus size: 102
160375 TGTTTCCCAT
* * * * *
160385 CAATTCATGGCACCC-GATGCCTAGGGGATATACCGAGGTATGTGAGCCTAGCTCTAGTTGGATT
1 CAATT-ATGGCACCCAG-TGCCAAGCGGATAAACCGCGATATGTGAGCCTAGCTCTAGTTGGATT
* * * * *
160449 ATCCAATGGTTTGCGCCTAGTGCTAGTTAGATAAATTGA
64 AACCAATGGTTTGCGCCCAGCGCTAGTAAGATAAACTGA
* *
160488 CAATTATGGCACCCAGTGCCAAGCGGATAAATCGCGATATGTGAGCCTAGCTCTGGTTGGATTAA
1 CAATTATGGCACCCAGTGCCAAGCGGATAAACCGCGATATGTGAGCCTAGCTCTAGTTGGATTAA
*
160553 CCAATGGTTTGTGCCCAGCGCTAGTAAGATAAACTGA
66 CCAATGGTTTGCGCCCAGCGCTAGTAAGATAAACTGA
* * * *
160590 CAGTTATGGCACCCAGTGTCTAGCGGATAAACCGTGATATGTGAGCC
1 CAATTATGGCACCCAGTGCCAAGCGGATAAACCGCGATATGTGAGCC
160637 CCAATCTAGC
Statistics
Matches: 130, Mismatches: 18, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
102 124 0.95
103 6 0.05
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.26
Consensus pattern (102 bp):
CAATTATGGCACCCAGTGCCAAGCGGATAAACCGCGATATGTGAGCCTAGCTCTAGTTGGATTAA
CCAATGGTTTGCGCCCAGCGCTAGTAAGATAAACTGA
Found at i:161200 original size:133 final size:133
Alignment explanation
Indices: 160962--161222 Score: 470
Period size: 133 Copynumber: 2.0 Consensus size: 133
160952 TCTTGCTCTC
160962 TATATATAACAATTCAAATCTTTCATTAATCCTTTGTATTCAACTCATATGCAACAATCCAAAAT
1 TATATATAACAATTCAAATCTTTCATTAATCCTTTGTATTCAACTCATATGCAACAATCCAAAAT
161027 GTTCAATATAATTCACATGGCAAGAAGCATTTATTTATTTATTTCCAGCCACCAAATATGCATAT
66 GTTCAATATAATTCACATGGCAAGAAGCATTTATTTATTTATTTCCAGCCACCAAATATGCATAT
161092 CAA
131 CAA
* **
161095 TATATATAACAATTCAAATCTTTCGTTAATCCTTTGTATTCAACTCATATTTAACAATCCAAAAT
1 TATATATAACAATTCAAATCTTTCATTAATCCTTTGTATTCAACTCATATGCAACAATCCAAAAT
*
161160 GTTCAATATAATTCACATGGTGAA-AAGCATTTATTTATTTATTTCCAGCCACCAAATATGCAT
66 GTTCAATATAATTCACATGG-CAAGAAGCATTTATTTATTTATTTCCAGCCACCAAATATGCAT
161223 TCCATCTAAC
Statistics
Matches: 123, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
133 121 0.98
134 2 0.02
ACGTcount: A:0.38, C:0.19, G:0.07, T:0.37
Consensus pattern (133 bp):
TATATATAACAATTCAAATCTTTCATTAATCCTTTGTATTCAACTCATATGCAACAATCCAAAAT
GTTCAATATAATTCACATGGCAAGAAGCATTTATTTATTTATTTCCAGCCACCAAATATGCATAT
CAA
Found at i:164397 original size:20 final size:19
Alignment explanation
Indices: 164357--164398 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
164347 TCTTTTATAA
*
164357 TTAACTTAATTAACCTTAC
1 TTAACTTAATTAACATTAC
164376 TTAAGCTTAATTAA-ATTCAC
1 TTAA-CTTAATTAACATT-AC
164396 TTA
1 TTA
164399 TTACATCACT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.38, C:0.17, G:0.02, T:0.43
Consensus pattern (19 bp):
TTAACTTAATTAACATTAC
Found at i:167117 original size:21 final size:21
Alignment explanation
Indices: 167082--167131 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
167072 ATAGTGTAGA
* * * *
167082 CTTCTACCGATACAAGTGAAG
1 CTTCTACTGAAACAAATCAAG
*
167103 CTTCTACTGAAACAAATCATG
1 CTTCTACTGAAACAAATCAAG
167124 CTTCTACT
1 CTTCTACT
167132 AGTACTAAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.32, C:0.26, G:0.12, T:0.30
Consensus pattern (21 bp):
CTTCTACTGAAACAAATCAAG
Found at i:169015 original size:20 final size:19
Alignment explanation
Indices: 168975--169016 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
168965 TCTTTTATAA
*
168975 TTAACTTAATTAACCTTAC
1 TTAACTTAATTAACATTAC
168994 TTAAGCTTAATTAA-ATTCAC
1 TTAA-CTTAATTAACATT-AC
169014 TTA
1 TTA
169017 TTACATCACT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.38, C:0.17, G:0.02, T:0.43
Consensus pattern (19 bp):
TTAACTTAATTAACATTAC
Found at i:171096 original size:34 final size:34
Alignment explanation
Indices: 171058--171207 Score: 135
Period size: 34 Copynumber: 4.5 Consensus size: 34
171048 ACACAGTTAA
* *
171058 CCATCCAACACACCAGATGCTTGTATGAGCCAAT
1 CCATCCAACACACCAAATGCTCGTATGAGCCAAT
* * * * *
171092 CCATCTAGCACACCAAATGCTTGTATCAGCTAAT
1 CCATCCAACACACCAAATGCTCGTATGAGCCAAT
* * * * *
171126 CCATCTAGCACACCAAATGCTCGTCTGAGCTAGT
1 CCATCCAACACACCAAATGCTCGTATGAGCCAAT
* * * *
171160 CCAACCAACACACCACACGCTCGTAAGAG-C--T
1 CCATCCAACACACCAAATGCTCGTATGAGCCAAT
171191 CCATCCAACACACCAAA
1 CCATCCAACACACCAAA
171208 ACACTATAAC
Statistics
Matches: 97, Mismatches: 19, Indels: 3
0.82 0.16 0.03
Matches are distributed among these distances:
31 16 0.16
34 81 0.84
ACGTcount: A:0.33, C:0.35, G:0.13, T:0.19
Consensus pattern (34 bp):
CCATCCAACACACCAAATGCTCGTATGAGCCAAT
Found at i:191849 original size:14 final size:15
Alignment explanation
Indices: 191830--191894 Score: 51
Period size: 15 Copynumber: 4.3 Consensus size: 15
191820 CCATTATACG
191830 AACTAT-AAATTGCA
1 AACTATGAAATTGCA
*
191844 AACTATGATATTGCA
1 AACTATGAAATTGCA
* *
191859 AGCTCTGCTAAATTGCA
1 AACTATG--AAATTGCA
* **
191876 AACTGTGATTTTGCA
1 AACTATGAAATTGCA
191891 AACT
1 AACT
191895 GTAATATGTT
Statistics
Matches: 40, Mismatches: 8, Indels: 5
0.75 0.15 0.09
Matches are distributed among these distances:
14 6 0.15
15 22 0.55
17 12 0.30
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Consensus pattern (15 bp):
AACTATGAAATTGCA
Found at i:193337 original size:18 final size:18
Alignment explanation
Indices: 193316--193351 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
193306 TGTTAGAAAT
193316 CCTACATTTAAAATTTAA
1 CCTACATTTAAAATTTAA
193334 CCTACATTTAAAATTTAA
1 CCTACATTTAAAATTTAA
193352 AATTAAAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.17, G:0.00, T:0.39
Consensus pattern (18 bp):
CCTACATTTAAAATTTAA
Found at i:197369 original size:52 final size:52
Alignment explanation
Indices: 197287--197395 Score: 209
Period size: 52 Copynumber: 2.1 Consensus size: 52
197277 GATGCTACCC
*
197287 AATGCATGGAATTCAGTAGGAGACCTAGATTGAAATATTTTACAATGGTTTG
1 AATGCATGGAATTCAGTAGGAGACCCAGATTGAAATATTTTACAATGGTTTG
197339 AATGCATGGAATTCAGTAGGAGACCCAGATTGAAATATTTTACAATGGTTTG
1 AATGCATGGAATTCAGTAGGAGACCCAGATTGAAATATTTTACAATGGTTTG
197391 AATGC
1 AATGC
197396 TCAAAATGAC
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 56 1.00
ACGTcount: A:0.35, C:0.11, G:0.23, T:0.31
Consensus pattern (52 bp):
AATGCATGGAATTCAGTAGGAGACCCAGATTGAAATATTTTACAATGGTTTG
Found at i:209424 original size:30 final size:29
Alignment explanation
Indices: 209390--209446 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 29
209380 AACAGGTCGG
*
209390 TCAAAGTCAATGGGTCGATCAACTGGTCAA
1 TCAAAGTCAATGGATCGATCAAC-GGTCAA
209420 TCAAAGTCAATGGATCGATCAACGGTC
1 TCAAAGTCAATGGATCGATCAACGGTC
209447 GGGGTCGAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 4 0.15
30 22 0.85
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.23
Consensus pattern (29 bp):
TCAAAGTCAATGGATCGATCAACGGTCAA
Found at i:210007 original size:20 final size:19
Alignment explanation
Indices: 209976--210014 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
209966 GGCTCATCGA
*
209976 AAAGGGAGAAAAATGAGAG
1 AAAGGGAGAAAAAGGAGAG
209995 AAAGGGAGAAAAAAGGAGAG
1 AAAGGGAG-AAAAAGGAGAG
210015 GTCGACTGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.59, C:0.00, G:0.38, T:0.03
Consensus pattern (19 bp):
AAAGGGAGAAAAAGGAGAG
Found at i:212974 original size:10 final size:10
Alignment explanation
Indices: 212943--212967 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
212933 AAGGACTTAA
212943 TTGGGAATTT
1 TTGGGAATTT
212953 TTGGGAATTT
1 TTGGGAATTT
212963 TTGGG
1 TTGGG
212968 GCTTTTTCGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.16, C:0.00, G:0.36, T:0.48
Consensus pattern (10 bp):
TTGGGAATTT
Found at i:213756 original size:7 final size:7
Alignment explanation
Indices: 213736--213827 Score: 98
Period size: 7 Copynumber: 13.1 Consensus size: 7
213726 TCGAATCGAC
213736 CCATTGA
1 CCATTGA
*
213743 CCGTTGA
1 CCATTGA
*
213750 TCATTGA
1 CCATTGA
213757 -CAGTTGA
1 CCA-TTGA
213764 CCATTGA
1 CCATTGA
213771 CCATTGA
1 CCATTGA
213778 CCATTGA
1 CCATTGA
213785 CCATTGA
1 CCATTGA
213792 CCATTGA
1 CCATTGA
*
213799 -TAGTTGA
1 CCA-TTGA
213806 CCATTGA
1 CCATTGA
**
213813 CTGTTGA
1 CCATTGA
*
213820 TCATTGA
1 CCATTGA
213827 C
1 C
213828 AGTTGACCGT
Statistics
Matches: 70, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
6 3 0.04
7 64 0.91
8 3 0.04
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (7 bp):
CCATTGA
Found at i:213756 original size:14 final size:14
Alignment explanation
Indices: 213736--213861 Score: 128
Period size: 14 Copynumber: 9.1 Consensus size: 14
213726 TCGAATCGAC
213736 CCATTGACCGTTGA
1 CCATTGACCGTTGA
* *
213750 TCATTGACAGTTGA
1 CCATTGACCGTTGA
*
213764 CCATTGACCATTGA
1 CCATTGACCGTTGA
*
213778 CCATTGACCATTGA
1 CCATTGACCGTTGA
**
213792 CCATTGATAGTTGA
1 CCATTGACCGTTGA
*
213806 CCATTGACTGTTGA
1 CCATTGACCGTTGA
* *
213820 TCATTGACAGTTGA
1 CCATTGACCGTTGA
* *
213834 CCGTTCACCGTTGA
1 CCATTGACCGTTGA
* *
213848 -CTTTGACTGTTGA
1 CCATTGACCGTTGA
213861 C
1 C
213862 TTTTTCTGAG
Statistics
Matches: 92, Mismatches: 19, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
13 10 0.11
14 82 0.89
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.33
Consensus pattern (14 bp):
CCATTGACCGTTGA
Found at i:220917 original size:7 final size:7
Alignment explanation
Indices: 220905--220939 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
220895 CGAACCGACT
220905 CGTTGAC
1 CGTTGAC
220912 CGTTGAC
1 CGTTGAC
*
220919 CGTTAAC
1 CGTTGAC
*
220926 CGTTAAC
1 CGTTGAC
220933 CGTTGAC
1 CGTTGAC
220940 TTTTTTCGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.20, C:0.29, G:0.23, T:0.29
Consensus pattern (7 bp):
CGTTGAC
Found at i:223296 original size:20 final size:19
Alignment explanation
Indices: 223262--223299 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
223252 GCTTGTAAAA
*
223262 AAAGGGAGAAAAAGGAGAG
1 AAAGCGAGAAAAAGGAGAG
223281 AAAGCGAGAGAAAAGGAGA
1 AAAGCGAGA-AAAAGGAGA
223300 TGTCGGATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.58, C:0.03, G:0.39, T:0.00
Consensus pattern (19 bp):
AAAGCGAGAAAAAGGAGAG
Found at i:224003 original size:41 final size:41
Alignment explanation
Indices: 223952--224042 Score: 119
Period size: 41 Copynumber: 2.2 Consensus size: 41
223942 CGCAAAAGGT
* * *
223952 AAAGCATTAGCGGCACTTATGGGAAAGCGCCGCTAAAGATC
1 AAAGCATTAGCGACACTTATAGCAAAGCGCCGCTAAAGATC
* ** *
223993 AGAGCATTAGCGATGCTTATAGCAAAGCGCCGCTAAAGGTC
1 AAAGCATTAGCGACACTTATAGCAAAGCGCCGCTAAAGATC
224034 AAAGCATTA
1 AAAGCATTA
224043 TAAGTGCCGC
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.35, C:0.21, G:0.25, T:0.19
Consensus pattern (41 bp):
AAAGCATTAGCGACACTTATAGCAAAGCGCCGCTAAAGATC
Done.